From f2ae4dc255bd86438cffb62c138326b1c0b5725f Mon Sep 17 00:00:00 2001
From: Dean Camera <dean@fourwalledcubicle.com>
Date: Sun, 20 May 2012 10:55:59 +0000
Subject: [PATCH] Upgrade Doxygen configuration files for Doxygen 1.8.1, fix
 broken stylesheet and footer HTML, add explicit spacing into documentation
 code fragments to prevent Doxygen from removing empty lines in the output.

---
 Bootloaders/CDC/BootloaderCDC.txt             |  8 +-
 Bootloaders/CDC/Doxygen.conf                  | 36 ++++-----
 Bootloaders/DFU/BootloaderDFU.txt             |  8 +-
 Bootloaders/DFU/Doxygen.conf                  | 36 ++++-----
 Bootloaders/HID/Doxygen.conf                  | 36 ++++-----
 .../ClassDriver/AudioInput/Doxygen.conf       | 36 ++++-----
 .../ClassDriver/AudioOutput/Doxygen.conf      | 36 ++++-----
 .../DualVirtualSerial/Doxygen.conf            | 36 ++++-----
 .../ClassDriver/GenericHID/Doxygen.conf       | 36 ++++-----
 .../Device/ClassDriver/Joystick/Doxygen.conf  | 36 ++++-----
 .../Device/ClassDriver/Keyboard/Doxygen.conf  | 36 ++++-----
 .../ClassDriver/KeyboardMouse/Doxygen.conf    | 36 ++++-----
 .../KeyboardMouseMultiReport/Doxygen.conf     | 36 ++++-----
 Demos/Device/ClassDriver/MIDI/Doxygen.conf    | 36 ++++-----
 .../ClassDriver/MassStorage/Doxygen.conf      | 36 ++++-----
 .../MassStorageKeyboard/Doxygen.conf          | 36 ++++-----
 Demos/Device/ClassDriver/Mouse/Doxygen.conf   | 36 ++++-----
 .../ClassDriver/RNDISEthernet/Doxygen.conf    | 36 ++++-----
 .../ClassDriver/VirtualSerial/Doxygen.conf    | 36 ++++-----
 .../VirtualSerialMassStorage/Doxygen.conf     | 36 ++++-----
 .../VirtualSerialMouse/Doxygen.conf           | 36 ++++-----
 Demos/Device/LowLevel/AudioInput/Doxygen.conf | 36 ++++-----
 .../Device/LowLevel/AudioOutput/Doxygen.conf  | 36 ++++-----
 .../LowLevel/DualVirtualSerial/Doxygen.conf   | 36 ++++-----
 Demos/Device/LowLevel/GenericHID/Doxygen.conf | 36 ++++-----
 Demos/Device/LowLevel/Joystick/Doxygen.conf   | 36 ++++-----
 Demos/Device/LowLevel/Keyboard/Doxygen.conf   | 36 ++++-----
 .../LowLevel/KeyboardMouse/Doxygen.conf       | 36 ++++-----
 Demos/Device/LowLevel/MIDI/Doxygen.conf       | 36 ++++-----
 .../Device/LowLevel/MassStorage/Doxygen.conf  | 36 ++++-----
 Demos/Device/LowLevel/Mouse/Doxygen.conf      | 36 ++++-----
 .../LowLevel/RNDISEthernet/Doxygen.conf       | 36 ++++-----
 .../LowLevel/VirtualSerial/Doxygen.conf       | 36 ++++-----
 .../ClassDriver/MouseHostDevice/Doxygen.conf  | 36 ++++-----
 .../AndroidAccessoryHost/Doxygen.conf         | 36 ++++-----
 .../ClassDriver/AudioInputHost/Doxygen.conf   | 36 ++++-----
 .../ClassDriver/AudioOutputHost/Doxygen.conf  | 36 ++++-----
 .../JoystickHostWithParser/Doxygen.conf       | 36 ++++-----
 .../ClassDriver/KeyboardHost/Doxygen.conf     | 36 ++++-----
 .../KeyboardHostWithParser/Doxygen.conf       | 36 ++++-----
 Demos/Host/ClassDriver/MIDIHost/Doxygen.conf  | 36 ++++-----
 .../ClassDriver/MassStorageHost/Doxygen.conf  | 36 ++++-----
 Demos/Host/ClassDriver/MouseHost/Doxygen.conf | 36 ++++-----
 .../MouseHostWithParser/Doxygen.conf          | 36 ++++-----
 .../Host/ClassDriver/PrinterHost/Doxygen.conf | 36 ++++-----
 .../RNDISEthernetHost/Doxygen.conf            | 36 ++++-----
 .../ClassDriver/StillImageHost/Doxygen.conf   | 36 ++++-----
 .../VirtualSerialHost/Doxygen.conf            | 36 ++++-----
 .../Incomplete/BluetoothHost/Doxygen.conf     | 36 ++++-----
 .../AndroidAccessoryHost/Doxygen.conf         | 36 ++++-----
 .../Host/LowLevel/AudioInputHost/Doxygen.conf | 36 ++++-----
 .../LowLevel/AudioOutputHost/Doxygen.conf     | 36 ++++-----
 .../Host/LowLevel/GenericHIDHost/Doxygen.conf | 36 ++++-----
 .../JoystickHostWithParser/Doxygen.conf       | 36 ++++-----
 Demos/Host/LowLevel/KeyboardHost/Doxygen.conf | 36 ++++-----
 .../KeyboardHostWithParser/Doxygen.conf       | 36 ++++-----
 Demos/Host/LowLevel/MIDIHost/Doxygen.conf     | 36 ++++-----
 .../LowLevel/MassStorageHost/Doxygen.conf     | 36 ++++-----
 Demos/Host/LowLevel/MouseHost/Doxygen.conf    | 36 ++++-----
 .../LowLevel/MouseHostWithParser/Doxygen.conf | 36 ++++-----
 Demos/Host/LowLevel/PrinterHost/Doxygen.conf  | 36 ++++-----
 .../LowLevel/RNDISEthernetHost/Doxygen.conf   | 36 ++++-----
 .../Host/LowLevel/StillImageHost/Doxygen.conf | 36 ++++-----
 .../LowLevel/VirtualSerialHost/Doxygen.conf   | 36 ++++-----
 LUFA/Doxygen.conf                             | 32 ++++----
 LUFA/DoxygenPages/SoftwareBootloaderJump.txt  | 16 ++--
 LUFA/DoxygenPages/Style/Footer.htm            | 30 ++++++--
 LUFA/DoxygenPages/Style/Style.css             | 77 +++++++++++++------
 LUFA/Drivers/Board/Buttons.h                  |  6 +-
 LUFA/Drivers/Board/Dataflash.h                | 20 ++---
 LUFA/Drivers/Board/Joystick.h                 | 12 +--
 LUFA/Drivers/Board/LEDs.h                     |  6 +-
 LUFA/Drivers/Board/Temperature.h              |  2 +-
 LUFA/Drivers/Misc/RingBuffer.h                | 10 +--
 LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h       |  6 +-
 LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h       |  6 +-
 LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h |  6 +-
 LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h    |  4 +-
 LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h       | 22 +++---
 LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h     |  6 +-
 .../Peripheral/XMEGA/SerialSPI_XMEGA.h        |  6 +-
 LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h  |  4 +-
 .../USB/Core/AVR8/EndpointStream_AVR8.h       | 20 ++---
 LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h  | 24 +++---
 LUFA/Drivers/USB/Core/ConfigDescriptor.h      |  9 ++-
 .../Drivers/USB/Core/UC3/EndpointStream_UC3.h | 24 +++---
 LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h    | 26 +++----
 .../USB/Core/XMEGA/EndpointStream_XMEGA.h     | 24 +++---
 LUFA/Drivers/USB/USB.h                        | 24 +++---
 LUFA/Platform/UC3/ClockManagement.h           |  6 +-
 LUFA/Platform/UC3/InterruptManagement.h       |  4 +-
 LUFA/Platform/XMEGA/ClockManagement.h         |  4 +-
 Projects/AVRISP-MKII/Doxygen.conf             | 36 ++++-----
 Projects/Benito/Doxygen.conf                  | 36 ++++-----
 Projects/HIDReportViewer/Doxygen.conf         | 36 ++++-----
 Projects/LEDNotifier/Doxygen.conf             | 36 ++++-----
 Projects/MIDIToneGenerator/Doxygen.conf       | 36 ++++-----
 Projects/Magstripe/Doxygen.conf               | 36 ++++-----
 Projects/MediaController/Doxygen.conf         | 36 ++++-----
 Projects/MissileLauncher/Doxygen.conf         | 36 ++++-----
 Projects/RelayBoard/Doxygen.conf              | 36 ++++-----
 Projects/SerialToLCD/Doxygen.conf             | 36 ++++-----
 Projects/TempDataLogger/Doxygen.conf          | 36 ++++-----
 Projects/USBtoSerial/Doxygen.conf             | 36 ++++-----
 Projects/Webserver/Doxygen.conf               | 36 ++++-----
 Projects/XPLAINBridge/Doxygen.conf            | 36 ++++-----
 106 files changed, 1388 insertions(+), 1800 deletions(-)

diff --git a/Bootloaders/CDC/BootloaderCDC.txt b/Bootloaders/CDC/BootloaderCDC.txt
index e88a7fba8..a3f74f3e3 100644
--- a/Bootloaders/CDC/BootloaderCDC.txt
+++ b/Bootloaders/CDC/BootloaderCDC.txt
@@ -98,7 +98,7 @@
  *  #define BOOTLOADER_API_TABLE_SIZE          32
  *  #define BOOTLOADER_API_TABLE_START         ((FLASHEND + 1UL) - BOOTLOADER_API_TABLE_SIZE)
  *  #define BOOTLOADER_API_CALL(Index)         (void*)((BOOTLOADER_API_TABLE_START + (Index * 2)) / 2)
- *
+ *  
  *  void    (*BootloaderAPI_ErasePage)(uint32_t Address)               = BOOTLOADER_API_CALL(0);
  *  void    (*BootloaderAPI_WritePage)(uint32_t Address)               = BOOTLOADER_API_CALL(1);
  *  void    (*BootloaderAPI_FillWord)(uint32_t Address, uint16_t Word) = BOOTLOADER_API_CALL(2);
@@ -106,13 +106,13 @@
  *  uint8_t (*BootloaderAPI_ReadFuse)(uint16_t Address)                = BOOTLOADER_API_CALL(4);
  *  uint8_t (*BootloaderAPI_ReadLock)(void)                            = BOOTLOADER_API_CALL(5);
  *  void    (*BootloaderAPI_WriteLock)(uint8_t LockBits)               = BOOTLOADER_API_CALL(6);
- *
+ *  
  *  #define BOOTLOADER_MAGIC_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 2))
  *  #define BOOTLOADER_MAGIC_SIGNATURE         0xDCFB
- *
+ *  
  *  #define BOOTLOADER_CLASS_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 4))
  *  #define BOOTLOADER_CDC_SIGNATURE           0xCDC1
- *
+ *  
  *  #define BOOTLOADER_ADDRESS_START           (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 8))
  *  #define BOOTLOADER_ADDRESS_LENGTH          4
  *  \endcode
diff --git a/Bootloaders/CDC/Doxygen.conf b/Bootloaders/CDC/Doxygen.conf
index b03ff0bc0..ea21cd05e 100644
--- a/Bootloaders/CDC/Doxygen.conf
+++ b/Bootloaders/CDC/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - CDC Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Bootloaders/DFU/BootloaderDFU.txt b/Bootloaders/DFU/BootloaderDFU.txt
index 13dd05b63..a01b1d9fd 100644
--- a/Bootloaders/DFU/BootloaderDFU.txt
+++ b/Bootloaders/DFU/BootloaderDFU.txt
@@ -103,7 +103,7 @@
  *  #define BOOTLOADER_API_TABLE_SIZE          32
  *  #define BOOTLOADER_API_TABLE_START         ((FLASHEND + 1UL) - BOOTLOADER_API_TABLE_SIZE)
  *  #define BOOTLOADER_API_CALL(Index)         (void*)((BOOTLOADER_API_TABLE_START + (Index * 2)) / 2)
- *
+ *  
  *  void    (*BootloaderAPI_ErasePage)(uint32_t Address)               = BOOTLOADER_API_CALL(0);
  *  void    (*BootloaderAPI_WritePage)(uint32_t Address)               = BOOTLOADER_API_CALL(1);
  *  void    (*BootloaderAPI_FillWord)(uint32_t Address, uint16_t Word) = BOOTLOADER_API_CALL(2);
@@ -111,13 +111,13 @@
  *  uint8_t (*BootloaderAPI_ReadFuse)(uint16_t Address)                = BOOTLOADER_API_CALL(4);
  *  uint8_t (*BootloaderAPI_ReadLock)(void)                            = BOOTLOADER_API_CALL(5);
  *  void    (*BootloaderAPI_WriteLock)(uint8_t LockBits)               = BOOTLOADER_API_CALL(6);
- *
+ *  
  *  #define BOOTLOADER_MAGIC_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 2))
  *  #define BOOTLOADER_MAGIC_SIGNATURE         0xDCFB
- *
+ *  
  *  #define BOOTLOADER_CLASS_SIGNATURE_START   (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 4))
  *  #define BOOTLOADER_CDC_SIGNATURE           0xDFB1
- *
+ *  
  *  #define BOOTLOADER_ADDRESS_START           (BOOTLOADER_API_TABLE_START + (BOOTLOADER_API_TABLE_SIZE - 8))
  *  #define BOOTLOADER_ADDRESS_LENGTH          4
  *  \endcode
diff --git a/Bootloaders/DFU/Doxygen.conf b/Bootloaders/DFU/Doxygen.conf
index 7739a7ed8..9aec702f5 100644
--- a/Bootloaders/DFU/Doxygen.conf
+++ b/Bootloaders/DFU/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - DFU Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Bootloaders/HID/Doxygen.conf b/Bootloaders/HID/Doxygen.conf
index bce70d62d..5fe5a69b8 100644
--- a/Bootloaders/HID/Doxygen.conf
+++ b/Bootloaders/HID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - HID Class Bootloader"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1727,7 +1721,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
index 3d3345971..d217aa443 100644
--- a/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioInput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
index 392086e96..4cd9e9c5b 100644
--- a/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
+++ b/Demos/Device/ClassDriver/AudioOutput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf b/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
index 3c9c10e2f..0f78680c3 100644
--- a/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
+++ b/Demos/Device/ClassDriver/DualVirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Dual Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
index 78e4ff04a..7b71c2054 100644
--- a/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
+++ b/Demos/Device/ClassDriver/GenericHID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Joystick/Doxygen.conf b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
index 348faaf11..407d08a86 100644
--- a/Demos/Device/ClassDriver/Joystick/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Joystick/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
index 57095df3d..0b47b1a32 100644
--- a/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Keyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
index 4016a2e42..a7357cb18 100644
--- a/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/KeyboardMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf b/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
index b0ed4dc40..c3696bbd9 100644
--- a/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
+++ b/Demos/Device/ClassDriver/KeyboardMouseMultiReport/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse (Multiple HID R
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MIDI/Doxygen.conf b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
index d17ed60c7..f95325f80 100644
--- a/Demos/Device/ClassDriver/MIDI/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MIDI/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
index 9da2792a0..4ef067503 100644
--- a/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf b/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
index cf8be4ea5..4f8b9e59d 100644
--- a/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
+++ b/Demos/Device/ClassDriver/MassStorageKeyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Mass Storage and Keyboard Devi
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/Mouse/Doxygen.conf b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
index d92f7f637..1dd2ccd02 100644
--- a/Demos/Device/ClassDriver/Mouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/Mouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
index 1da1f868b..da74f6b48 100644
--- a/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/ClassDriver/RNDISEthernet/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
index 2cd6e221e..ebe72a5d9 100644
--- a/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
index c507f2691..c38f51df6 100644
--- a/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerialMassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial/Mass Storage Device Demo
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf b/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
index 6aaf97067..fea97b2d9 100644
--- a/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
+++ b/Demos/Device/ClassDriver/VirtualSerialMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Virtual Serial and Mouse Devic
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/AudioInput/Doxygen.conf b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
index 3d3345971..d217aa443 100644
--- a/Demos/Device/LowLevel/AudioInput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioInput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
index 392086e96..4cd9e9c5b 100644
--- a/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
+++ b/Demos/Device/LowLevel/AudioOutput/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf b/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
index 3c9c10e2f..0f78680c3 100644
--- a/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
+++ b/Demos/Device/LowLevel/DualVirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Dual Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/GenericHID/Doxygen.conf b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
index 78e4ff04a..7b71c2054 100644
--- a/Demos/Device/LowLevel/GenericHID/Doxygen.conf
+++ b/Demos/Device/LowLevel/GenericHID/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Joystick/Doxygen.conf b/Demos/Device/LowLevel/Joystick/Doxygen.conf
index 348faaf11..407d08a86 100644
--- a/Demos/Device/LowLevel/Joystick/Doxygen.conf
+++ b/Demos/Device/LowLevel/Joystick/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Keyboard/Doxygen.conf b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
index 57095df3d..0b47b1a32 100644
--- a/Demos/Device/LowLevel/Keyboard/Doxygen.conf
+++ b/Demos/Device/LowLevel/Keyboard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
index 4016a2e42..a7357cb18 100644
--- a/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/KeyboardMouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Combined Keyboard/Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/MIDI/Doxygen.conf b/Demos/Device/LowLevel/MIDI/Doxygen.conf
index d17ed60c7..f95325f80 100644
--- a/Demos/Device/LowLevel/MIDI/Doxygen.conf
+++ b/Demos/Device/LowLevel/MIDI/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/MassStorage/Doxygen.conf b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
index 9da2792a0..4ef067503 100644
--- a/Demos/Device/LowLevel/MassStorage/Doxygen.conf
+++ b/Demos/Device/LowLevel/MassStorage/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/Mouse/Doxygen.conf b/Demos/Device/LowLevel/Mouse/Doxygen.conf
index d92f7f637..1dd2ccd02 100644
--- a/Demos/Device/LowLevel/Mouse/Doxygen.conf
+++ b/Demos/Device/LowLevel/Mouse/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
index 1da1f868b..da74f6b48 100644
--- a/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
+++ b/Demos/Device/LowLevel/RNDISEthernet/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf b/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
index 2cd6e221e..ebe72a5d9 100644
--- a/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
+++ b/Demos/Device/LowLevel/VirtualSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Device Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf b/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
index 8a3662e90..ec511fec4 100644
--- a/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
+++ b/Demos/DualRole/ClassDriver/MouseHostDevice/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host/Device Dual Role Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf b/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
index 7c75b5228..36cb2f08e 100644
--- a/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AndroidAccessoryHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Android Accessory Mode Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf b/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
index af07c395d..f3ed928f6 100644
--- a/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AudioInputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf b/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
index 8255519a3..237d312e6 100644
--- a/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/AudioOutputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
index c7c037a84..575abd0e3 100644
--- a/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/JoystickHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf b/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
index 2557f3305..e626e69be 100644
--- a/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/KeyboardHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
index 00a850d38..72a0fb759 100644
--- a/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/KeyboardHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf b/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
index 321cffdd4..1d898aca2 100644
--- a/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MIDIHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf b/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
index 2522f53fd..086bf674c 100644
--- a/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MassStorageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MouseHost/Doxygen.conf b/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
index 618c4d84b..29459d8bc 100644
--- a/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MouseHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf b/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
index b2370b965..35b3dd063 100644
--- a/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
+++ b/Demos/Host/ClassDriver/MouseHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo (Using HID Descriptor P
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf b/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
index 791fe7293..af83229fb 100644
--- a/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/PrinterHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Printer Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf b/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
index 9b89a5dad..8864c18da 100644
--- a/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/RNDISEthernetHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Ethernet Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf b/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
index 6341892c0..f9ebf1510 100644
--- a/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/StillImageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Still Image Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf b/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
index 852d288b7..d6fe34d79 100644
--- a/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
+++ b/Demos/Host/ClassDriver/VirtualSerialHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf b/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
index 84704812b..f4d15a6cf 100644
--- a/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
+++ b/Demos/Host/Incomplete/BluetoothHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Bluetooth Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf b/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
index 7c75b5228..36cb2f08e 100644
--- a/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AndroidAccessoryHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Android Accessory Mode Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf b/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
index af07c395d..f3ed928f6 100644
--- a/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AudioInputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Input Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf b/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
index 8255519a3..237d312e6 100644
--- a/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/AudioOutputHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Audio Output Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
index d9685efd2..ae6cafac0 100644
--- a/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/GenericHIDHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Generic HID Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
index c7c037a84..575abd0e3 100644
--- a/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/JoystickHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Joystick Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
index 2557f3305..e626e69be 100644
--- a/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
index 00a850d38..72a0fb759 100644
--- a/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/KeyboardHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Keyboard Host Demo (Using HID Descripto
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MIDIHost/Doxygen.conf b/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
index 321cffdd4..1d898aca2 100644
--- a/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MIDIHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
index 2522f53fd..086bf674c 100644
--- a/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MassStorageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mass Storage Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MouseHost/Doxygen.conf b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
index 618c4d84b..29459d8bc 100644
--- a/Demos/Host/LowLevel/MouseHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
index b2370b965..35b3dd063 100644
--- a/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
+++ b/Demos/Host/LowLevel/MouseHostWithParser/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Mouse Host Demo (Using HID Descriptor P
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
index 791fe7293..af83229fb 100644
--- a/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/PrinterHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Printer Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf b/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
index 78a37f24b..dac7bf3c0 100644
--- a/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/RNDISEthernetHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - RNDIS Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
index 6341892c0..f9ebf1510 100644
--- a/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/StillImageHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Still Image Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf b/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
index 852d288b7..d6fe34d79 100644
--- a/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
+++ b/Demos/Host/LowLevel/VirtualSerialHost/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Virtual Serial Host Demo"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/LUFA/Doxygen.conf b/LUFA/Doxygen.conf
index 0edee54cd..5c3bf65b8 100644
--- a/LUFA/Doxygen.conf
+++ b/LUFA/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 15
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = YES
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1727,7 +1721,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/LUFA/DoxygenPages/SoftwareBootloaderJump.txt b/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
index 1fad85fb7..09de9234d 100644
--- a/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
+++ b/LUFA/DoxygenPages/SoftwareBootloaderJump.txt
@@ -25,15 +25,15 @@
  *  #include <avr/wdt.h>
  *  #include <avr/io.h>
  *  #include <util/delay.h>
- *
+ *  
  *  #include <LUFA/Common/Common.h>
  *  #include <LUFA/Drivers/USB/USB.h>
- *
+ *  
  *  uint32_t Boot_Key ATTR_NO_INIT;
- *
+ *  
  *  #define MAGIC_BOOT_KEY            0xDC42ACCA
  *  #define BOOTLOADER_START_ADDRESS  (FLASH_SIZE_BYTES - BOOTLOADER_SEC_SIZE_BYTES)
- *
+ *  
  *  void Bootloader_Jump_Check(void) ATTR_INIT_SECTION(3);
  *  void Bootloader_Jump_Check(void)
  *  {
@@ -44,18 +44,18 @@
  *          ((void (*)(void))BOOTLOADER_START_ADDRESS)();
  *      }
  *  }
- *
+ *  
  *  void Jump_To_Bootloader(void)
  *  {
  *      // If USB is used, detach from the bus and reset it
  *      USB_Disable();
- *
+ *      
  *      // Disable all interrupts
  *      cli();
- *
+ *      
  *      // Wait two seconds for the USB detachment to register on the host
  *      Delay_MS(2000);
- *
+ *      
  *      // Set the bootloader key to the magic value and force a reset
  *      Boot_Key = MAGIC_BOOT_KEY;
  *      wdt_enable(WDTO_250MS);
diff --git a/LUFA/DoxygenPages/Style/Footer.htm b/LUFA/DoxygenPages/Style/Footer.htm
index 70bce5313..a72c5bdd2 100644
--- a/LUFA/DoxygenPages/Style/Footer.htm
+++ b/LUFA/DoxygenPages/Style/Footer.htm
@@ -1,15 +1,35 @@
 <!--BEGIN GENERATE_TREEVIEW-->
-			<span style="margin-right: 20px; float: right;">
+	<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+		<ul>
+			<li class="footer" style="float:left !important;">
+				$generatedby
+				<a href="http://www.doxygen.org/index.html">
+					<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+				</a>
+				$doxygenversion
+			</li>
+
+			<li class="footer">
 				<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
-			</span>
+			</li>
 		</ul>
 	</div>
 <!--END GENERATE_TREEVIEW-->
 <!--BEGIN !GENERATE_TREEVIEW-->
 		<hr class="footer"/>
-		<span style="margin-right: 20px; float: right;">
-			<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
-		</span>
+		<div class="footer">
+			<span style="float: left;">
+				$generatedby
+				<a href="http://www.doxygen.org/index.html">
+					<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+				</a>
+				$doxygenversion
+			</span>
+
+			<span style="margin-right: 20px; float: right;">
+				<a href="http://www.lufa-lib.org" title="LUFA Project Page">LUFA Project Page</a> | <a href="http://www.lufa-lib.org/support" title="LUFA Support List">Support Mailing List</a> | <a href="http://www.lufa-lib.org/donate" title="Donate to Support LUFA">Donate</a> | <a href="http://www.fourwalledcubicle.com" title="Four Walled Cubicle Website">Four Walled Cubicle</a> - LUFA, the Lightweight USB Framework for AVRs
+			</span>
+		</div>
 <!--END !GENERATE_TREEVIEW-->
 	</body>
 </html>
\ No newline at end of file
diff --git a/LUFA/DoxygenPages/Style/Style.css b/LUFA/DoxygenPages/Style/Style.css
index 3bff51e78..b64f9de83 100644
--- a/LUFA/DoxygenPages/Style/Style.css
+++ b/LUFA/DoxygenPages/Style/Style.css
@@ -43,14 +43,11 @@
 		overflow:inherit;
 		width:auto !important;
 	}
-
-	pre.fragment
+	
+	.fragment
 	{
-		overflow:visible;
-		text-wrap:unrestricted;
-		white-space:pre-wrap;
-		word-wrap:break-word;
-	}
+		background-color: #FFFFFF !important;
+	}	
 }
 
 body,table,div,p,dl
@@ -81,9 +78,8 @@ div.contents table.memberdecls,.paramname
 
 h1
 {
-	font-size:30px;
+	font-size:25px;
 	margin-bottom:10px;
-	padding:0 0 20px;
 }
 
 h2
@@ -228,22 +224,55 @@ dl.el
 	margin-left:-1cm;
 }
 
-.fragment
-{
-	font-family:monospace, fixed;
-	font-size:105%;
+pre.fragment {
+        border: 1px solid #C4CFE5;
+        background-color: #FBFCFD;
+        padding: 4px 6px;
+        margin: 4px 8px 4px 2px;
+        overflow: auto;
+        word-wrap: break-word;
+        font-size:  9pt;
+        line-height: 125%;
+        font-family: monospace, fixed;
+        font-size: 105%;
 }
 
-pre.fragment
-{
-	background-color:#F8F8F8;
-	border:1px solid #C1CEE8;
-	font-size:10pt;
-	line-height:125%;
-	margin:4px 8px 4px 20px;
-	overflow:auto;
-	padding:4px 6px;
-	word-wrap:break-word;
+div.fragment {
+	padding: 4px;
+	margin: 4px;
+	background-color: #FBFCFD;
+	border: 1px solid #C4CFE5;
+}
+
+div.line {
+	font-family: monospace, fixed;
+	font-size: 13px;
+	line-height: 1.0;
+	text-wrap: unrestricted;
+	white-space: -moz-pre-wrap; /* Moz */
+	white-space: -pre-wrap;     /* Opera 4-6 */
+	white-space: -o-pre-wrap;   /* Opera 7 */
+	white-space: pre-wrap;      /* CSS3  */
+	word-wrap: break-word;      /* IE 5.5+ */
+	text-indent: -53px;
+	padding-left: 53px;
+	padding-bottom: 0px;
+	margin: 0px;
+}
+
+span.lineno {
+	padding-right: 4px;
+	text-align: right;
+	border-right: 2px solid #0F0;
+	background-color: #E8E8E8;
+	white-space: pre;
+}
+span.lineno a {
+	background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+	background-color: #C8C8C8;
 }
 
 div.ah
@@ -1090,4 +1119,4 @@ div.toc li.level3
 div.toc li.level4
 {
 	margin-left:45px;
-}
\ No newline at end of file
+}
diff --git a/LUFA/Drivers/Board/Buttons.h b/LUFA/Drivers/Board/Buttons.h
index c3d6c0d00..1b70a6bd5 100644
--- a/LUFA/Drivers/Board/Buttons.h
+++ b/LUFA/Drivers/Board/Buttons.h
@@ -68,13 +68,13 @@
  *  \code
  *      // Initialize the button driver before first use
  *      Buttons_Init();
- *
+ *      
  *      printf("Waiting for button press...\r\n");
- *
+ *      
  *      // Loop until a board button has been pressed
  *      uint8_t ButtonPress;
  *      while (!(ButtonPress = Buttons_GetStatus())) {};
- *
+ *      
  *      // Display which button was pressed (assuming two board buttons)
  *      printf("Button pressed: %s\r\n", (ButtonPress == BUTTONS_BUTTON1) ? "Button 1" : "Button 2");
  *  \endcode
diff --git a/LUFA/Drivers/Board/Dataflash.h b/LUFA/Drivers/Board/Dataflash.h
index a5ae29dc8..c9f66054b 100644
--- a/LUFA/Drivers/Board/Dataflash.h
+++ b/LUFA/Drivers/Board/Dataflash.h
@@ -70,44 +70,44 @@
  *      SPI_Init(SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
  *      Dataflash_Init();
- *
+ *      
  *      uint8_t WriteBuffer[DATAFLASH_PAGE_SIZE];
  *      uint8_t ReadBuffer[DATAFLASH_PAGE_SIZE];
- *
+ *      
  *      // Fill page write buffer with a repeating pattern
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        WriteBuffer[i] = (i & 0xFF);
- *
+ *      
  *      // Must select the chip of interest first before operating on it
  *      Dataflash_SelectChip(DATAFLASH_CHIP1);
- *
+ *      
  *      // Write to the Dataflash's first internal memory buffer
  *      printf("Writing data to first dataflash buffer:\r\n");
  *      Dataflash_SendByte(DF_CMD_BUFF1WRITE);
  *      Dataflash_SendAddressBytes(0, 0);
- *
+ *      
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        Dataflash_SendByte(WriteBuffer[i]);
- *
+ *      
  *      // Commit the Dataflash's first memory buffer to the non-volatile FLASH memory
  *      printf("Committing page to non-volatile memory page index 5:\r\n");
  *      Dataflash_SendByte(DF_CMD_BUFF1TOMAINMEMWITHERASE);
  *      Dataflash_SendAddressBytes(5, 0);
  *      Dataflash_WaitWhileBusy();
- *
+ *      
  *      // Read the page from non-volatile FLASH memory into the Dataflash's second memory buffer
  *      printf("Reading data into second dataflash buffer:\r\n");
  *      Dataflash_SendByte(DF_CMD_MAINMEMTOBUFF2);
  *      Dataflash_SendAddressBytes(5, 0);
  *      Dataflash_WaitWhileBusy();
- *
+ *      
  *      // Read the Dataflash's second internal memory buffer
  *      Dataflash_SendByte(DF_CMD_BUFF2READ);
  *      Dataflash_SendAddressBytes(0, 0);
- *
+ *      
  *      for (uint16_t i = 0; i < DATAFLASH_PAGE_SIZE; i++)
  *        ReadBuffer[i] = Dataflash_ReceiveByte();
- *
+ *      
  *      // Deselect the chip after use
  *      Dataflash_DeselectChip();
  *  \endcode
diff --git a/LUFA/Drivers/Board/Joystick.h b/LUFA/Drivers/Board/Joystick.h
index 0a1f9fa7a..63d28e837 100644
--- a/LUFA/Drivers/Board/Joystick.h
+++ b/LUFA/Drivers/Board/Joystick.h
@@ -67,22 +67,22 @@
  *  \code
  *      // Initialize the board Joystick driver before first use
  *      Joystick_Init();
- *
+ *      
  *      printf("Waiting for joystick movement...\r\n");
- *
+ *      
  *      // Loop until a the joystick has been moved
  *      uint8_t JoystickMovement;
  *      while (!(JoystickMovement = Joystick_GetStatus())) {};
- *
+ *      
  *      // Display which direction the joystick was moved in
  *      printf("Joystick moved:\r\n");
- *
+ *      
  *      if (JoystickMovement & (JOY_UP | JOY_DOWN))
  *        printf("%s ", (JoystickMovement & JOY_UP) ? "Up" : "Down");
- *
+ *      
  *      if (JoystickMovement & (JOY_LEFT | JOY_RIGHT))
  *        printf("%s ", (JoystickMovement & JOY_LEFT) ? "Left" : "Right");
- *
+ *      
  *      if (JoystickMovement & JOY_PRESS)
  *        printf("Pressed");
  *  \endcode
diff --git a/LUFA/Drivers/Board/LEDs.h b/LUFA/Drivers/Board/LEDs.h
index f6f9d82ff..97cb81a50 100644
--- a/LUFA/Drivers/Board/LEDs.h
+++ b/LUFA/Drivers/Board/LEDs.h
@@ -76,7 +76,7 @@
  *  \code
  *      // Initialize the board LED driver before first use
  *      LEDs_Init();
- *
+ *      
  *      // Turn on each of the four LEDs in turn
  *      LEDs_SetAllLEDs(LEDS_LED1);
  *      Delay_MS(500);
@@ -86,11 +86,11 @@
  *      Delay_MS(500);
  *      LEDs_SetAllLEDs(LEDS_LED4);
  *      Delay_MS(500);
- *
+ *      
  *      // Turn on all LEDs
  *      LEDs_SetAllLEDs(LEDS_ALL_LEDS);
  *      Delay_MS(1000);
- *
+ *      
  *      // Turn on LED 1, turn off LED 2, leaving LEDs 3 and 4 in their current state
  *      LEDs_ChangeLEDs((LEDS_LED1 | LEDS_LED2), LEDS_LED1);
  *  \endcode
diff --git a/LUFA/Drivers/Board/Temperature.h b/LUFA/Drivers/Board/Temperature.h
index ef967967b..54ca957a6 100644
--- a/LUFA/Drivers/Board/Temperature.h
+++ b/LUFA/Drivers/Board/Temperature.h
@@ -56,7 +56,7 @@
  *      // Initialize the ADC and board temperature sensor drivers before first use
  *      ADC_Init(ADC_FREE_RUNNING | ADC_PRESCALE_128);
  *      Temperature_Init();
- *
+ *      
  *      // Display converted temperature in degrees Celsius
  *      printf("Current Temperature: %d Degrees\r\n", Temperature_GetTemperature());
  *  \endcode
diff --git a/LUFA/Drivers/Misc/RingBuffer.h b/LUFA/Drivers/Misc/RingBuffer.h
index df7e70218..b0bc5c55d 100644
--- a/LUFA/Drivers/Misc/RingBuffer.h
+++ b/LUFA/Drivers/Misc/RingBuffer.h
@@ -65,23 +65,23 @@
  *      // Create the buffer structure and its underlying storage array
  *      RingBuffer_t Buffer;
  *      uint8_t      BufferData[128];
- *
+ *      
  *      // Initialize the buffer with the created storage array
  *      RingBuffer_InitBuffer(&Buffer, BufferData, sizeof(BufferData));
- *
+ *      
  *      // Insert some data into the buffer
  *      RingBuffer_Insert(Buffer, 'H');
  *      RingBuffer_Insert(Buffer, 'E');
  *      RingBuffer_Insert(Buffer, 'L');
  *      RingBuffer_Insert(Buffer, 'L');
  *      RingBuffer_Insert(Buffer, 'O');
- *
+ *      
  *      // Cache the number of stored bytes in the buffer
  *      uint16_t BufferCount = RingBuffer_GetCount(&Buffer);
- *
+ *      
  *      // Printer stored data length
  *      printf("Buffer Length: %d, Buffer Data: \r\n", BufferCount);
- *
+ *      
  *      // Print contents of the buffer one character at a time
  *      while (BufferCount--)
  *        putc(RingBuffer_Remove(&Buffer));
diff --git a/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
index ec80dd247..c04d2ba8c 100644
--- a/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/ADC_AVR8.h
@@ -55,14 +55,14 @@
  *  \code
  *      // Initialize the ADC driver before first use
  *      ADC_Init(ADC_FREE_RUNNING | ADC_PRESCALE_32);
- *
+ *      
  *      // Must setup the ADC channel to read beforehand
  *      ADC_SetupChannel(1);
- *
+ *      
  *      // Perform a single conversion of the ADC channel 1
  *      ADC_GetChannelReading(ADC_REFERENCE_AVCC | ADC_RIGHT_ADJUSTED | ADC_CHANNEL1);
  *      printf("Conversion Result: %d\r\n", ADC_GetResult());
- *
+ *      
  *      // Start reading ADC channel 1 in free running (continuous conversion) mode
  *      ADC_StartReading(ADC_REFERENCE_AVCC | ADC_RIGHT_ADJUSTED | ADC_CHANNEL1);
  *      for (;;)
diff --git a/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
index 2e396ed55..3ca037606 100644
--- a/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/SPI_AVR8.h
@@ -56,17 +56,17 @@
  *      // Initialize the SPI driver before first use
  *      SPI_Init(SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SPI_SendByte(0x01);
  *      SPI_SendByte(0x02);
  *      SPI_SendByte(0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SPI_ReceiveByte();
  *      uint8_t Byte2 = SPI_ReceiveByte();
  *      uint8_t Byte3 = SPI_ReceiveByte();
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SPI_TransferByte(0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
index 562aaecfd..24d341f03 100644
--- a/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/SerialSPI_AVR8.h
@@ -53,17 +53,17 @@
  *  \code
  *      // Initialize the Master SPI mode USART driver before first use, with 1Mbit baud
  *      SerialSPI_Init((USART_SPI_SCK_LEAD_RISING | SPI_SAMPLE_LEADING | SPI_ORDER_MSB_FIRST), 1000000);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SerialSPI_SendByte(0x01);
  *      SerialSPI_SendByte(0x02);
  *      SerialSPI_SendByte(0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SerialSPI_ReceiveByte();
  *      uint8_t Byte2 = SerialSPI_ReceiveByte();
  *      uint8_t Byte3 = SerialSPI_ReceiveByte();
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SerialSPI_TransferByte(0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
index 687ea74ad..b7b50f434 100644
--- a/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/Serial_AVR8.h
@@ -53,10 +53,10 @@
  *  \code
  *      // Initialize the serial USART driver before first use, with 9600 baud (and no double-speed mode)
  *      Serial_Init(9600, false);
- *
+ *      
  *      // Send a string through the USART
  *      Serial_TxString("Test String\r\n");
- *
+ *      
  *      // Receive a byte through the USART
  *      uint8_t DataByte = Serial_RxByte();
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h b/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
index b9131df3c..38ad1f3e3 100644
--- a/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
+++ b/LUFA/Drivers/Peripheral/AVR8/TWI_AVR8.h
@@ -54,35 +54,35 @@
  *  \code
  *      // Initialize the TWI driver before first use at 200KHz
  *      TWI_Init(TWI_BIT_PRESCALE_1, TWI_BITLENGTH_FROM_FREQ(1, 200000));
- *
+ *      
  *      // Start a write session to device at device address 0xA0, internal address 0xDC with a 10ms timeout
  *      if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_WRITE, 10) == TWI_ERROR_NoError)
  *      {
  *          TWI_SendByte(0xDC);
- *
+ *          
  *          TWI_SendByte(0x01);
  *          TWI_SendByte(0x02);
  *          TWI_SendByte(0x03);
- *
+ *          
  *          // Must stop transmission afterwards to release the bus
  *          TWI_StopTransmission();
  *      }
- *
+ *      
  *      // Start a read session to device at address 0xA0, internal address 0xDC with a 10ms timeout
  *      if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_WRITE, 10) == TWI_ERROR_NoError)
  *      {
  *          TWI_SendByte(0xDC);
  *          TWI_StopTransmission();
- *
+ *          
  *          if (TWI_StartTransmission(0xA0 | TWI_ADDRESS_READ, 10) == TWI_ERROR_NoError)
  *          {
  *              uint8_t Byte1, Byte2, Byte3;
- *
+ *              
  *              // Read three bytes, acknowledge after the third byte is received
  *              TWI_ReceiveByte(&Byte1, false);
  *              TWI_ReceiveByte(&Byte2, false);
  *              TWI_ReceiveByte(&Byte3, true);
- *
+ *              
  *              // Must stop transmission afterwards to release the bus
  *              TWI_StopTransmission();
  *          }
@@ -93,18 +93,18 @@
  *  \code
  *      // Initialize the TWI driver before first use at 200KHz
  *      TWI_Init(TWI_BIT_PRESCALE_1, TWI_BITLENGTH_FROM_FREQ(1, 200000));
- *
+ *      
  *      // Start a write session to device at device address 0xA0, internal address 0xDC with a 10ms timeout
  *      uint8_t InternalWriteAddress = 0xDC;
  *      uint8_t WritePacket[3] = {0x01, 0x02, 0x03};
- *
+ *      
  *      TWI_WritePacket(0xA0, 10, &InternalWriteAddress, sizeof(InternalWriteAddress),
  *                      &WritePacket, sizeof(WritePacket);
- *
+ *      
  *      // Start a read session to device at address 0xA0, internal address 0xDC with a 10ms timeout
  *      uint8_t InternalReadAddress = 0xDC;
  *      uint8_t ReadPacket[3];
- *
+ *      
  *      TWI_ReadPacket(0xA0, 10, &InternalReadAddress, sizeof(InternalReadAddress),
  *                     &ReadPacket, sizeof(ReadPacket);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
index a21ac1ca8..8c57dacd9 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/SPI_XMEGA.h
@@ -53,17 +53,17 @@
  *      SPI_Init(&SPIC,
  *               SPI_SPEED_FCPU_DIV_2 | SPI_ORDER_MSB_FIRST | SPI_SCK_LEAD_FALLING |
  *               SPI_SAMPLE_TRAILING | SPI_MODE_MASTER);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SPI_SendByte(&SPIC, 0x01);
  *      SPI_SendByte(&SPIC, 0x02);
  *      SPI_SendByte(&SPIC, 0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SPI_ReceiveByte(&SPIC);
  *      uint8_t Byte2 = SPI_ReceiveByte(&SPIC);
  *      uint8_t Byte3 = SPI_ReceiveByte(&SPIC);
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SPI_TransferByte(&SPIC, 0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
index a0e9e3370..64d57a3f0 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/SerialSPI_XMEGA.h
@@ -53,17 +53,17 @@
  *  \code
  *      // Initialize the Master SPI mode USART driver before first use, with 1Mbit baud
  *      SerialSPI_Init(&USARTD0, (USART_SPI_SCK_LEAD_RISING | USART_SPI_SAMPLE_LEADING | USART_SPI_ORDER_MSB_FIRST), 1000000);
- *
+ *      
  *      // Send several bytes, ignoring the returned data
  *      SerialSPI_SendByte(&USARTD0, 0x01);
  *      SerialSPI_SendByte(&USARTD0, 0x02);
  *      SerialSPI_SendByte(&USARTD0, 0x03);
- *
+ *      
  *      // Receive several bytes, sending a dummy 0x00 byte each time
  *      uint8_t Byte1 = SerialSPI_ReceiveByte(&USARTD);
  *      uint8_t Byte2 = SerialSPI_ReceiveByte(&USARTD);
  *      uint8_t Byte3 = SerialSPI_ReceiveByte(&USARTD);
- *
+ *      
  *      // Send a byte, and store the received byte from the same transaction
  *      uint8_t ResponseByte = SerialSPI_TransferByte(&USARTD0, 0xDC);
  *  \endcode
diff --git a/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h b/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
index 283732f0f..c2cb77fd3 100644
--- a/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
+++ b/LUFA/Drivers/Peripheral/XMEGA/Serial_XMEGA.h
@@ -53,10 +53,10 @@
  *  \code
  *      // Initialize the serial USART driver before first use, with 9600 baud (and no double-speed mode)
  *      Serial_Init(&USARTD0, 9600, false);
- *
+ *      
  *      // Send a string through the USART
  *      Serial_TxString(&USARTD0, "Test String\r\n");
- *
+ *      
  *      // Receive a byte through the USART
  *      uint8_t DataByte = Serial_RxByte(&USARTD0);
  *  \endcode
diff --git a/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h b/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
index ecc1fb0b9..072d85932 100644
--- a/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
+++ b/LUFA/Drivers/USB/Core/AVR8/EndpointStream_AVR8.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -98,13 +98,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -151,13 +151,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -199,7 +199,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -276,7 +276,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
diff --git a/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h b/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
index e9da42256..53316f2f9 100644
--- a/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
+++ b/LUFA/Drivers/USB/Core/AVR8/PipeStream_AVR8.h
@@ -85,7 +85,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Discard_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -96,13 +96,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Discard_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -137,7 +137,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Null_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -148,13 +148,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Null_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -198,7 +198,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                        NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
@@ -211,14 +211,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                           &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -279,7 +279,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                       NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
@@ -292,14 +292,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                          &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
diff --git a/LUFA/Drivers/USB/Core/ConfigDescriptor.h b/LUFA/Drivers/USB/Core/ConfigDescriptor.h
index 5e97939e7..22e76cba9 100644
--- a/LUFA/Drivers/USB/Core/ConfigDescriptor.h
+++ b/LUFA/Drivers/USB/Core/ConfigDescriptor.h
@@ -76,7 +76,7 @@
 			 *  uint8_t* CurrDescriptor = &ConfigDescriptor[0]; // Pointing to the configuration header
 			 *  USB_Descriptor_Configuration_Header_t* ConfigHeaderPtr = DESCRIPTOR_PCAST(CurrDescriptor,
 			 *                                                           USB_Descriptor_Configuration_Header_t);
-			 *
+			 *  
 			 *  // Can now access elements of the configuration header struct using the -> indirection operator
 			 *  \endcode
 			 */
@@ -90,7 +90,7 @@
 			 *  uint8_t* CurrDescriptor = &ConfigDescriptor[0]; // Pointing to the configuration header
 			 *  USB_Descriptor_Configuration_Header_t ConfigHeader = DESCRIPTOR_CAST(CurrDescriptor,
 			 *                                                       USB_Descriptor_Configuration_Header_t);
-			 *
+			 *  
 			 *  // Can now access elements of the configuration header struct using the . operator
 			 *  \endcode
 			 */
@@ -231,7 +231,7 @@
 			 *  Usage Example:
 			 *  \code
 			 *  uint8_t EndpointSearcher(void* CurrentDescriptor); // Comparator Prototype
-			 *
+			 *  
 			 *  uint8_t EndpointSearcher(void* CurrentDescriptor)
 			 *  {
 			 *     if (DESCRIPTOR_TYPE(CurrentDescriptor) == DTYPE_Endpoint)
@@ -239,8 +239,9 @@
 			 *     else
 			 *         return DESCRIPTOR_SEARCH_NotFound;
 			 *  }
-			 *
+			 *  
 			 *  //...
+			 *  
 			 *  // After retrieving configuration descriptor:
 			 *  if (USB_Host_GetNextDescriptorComp(&BytesRemaining, &CurrentConfigLoc, EndpointSearcher) ==
 			 *      Descriptor_Search_Comp_Found)
diff --git a/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h b/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
index 335e19782..40a54ee17 100644
--- a/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
+++ b/LUFA/Drivers/USB/Core/UC3/EndpointStream_UC3.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -98,13 +98,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -151,13 +151,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -199,7 +199,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -212,14 +212,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                               &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -276,7 +276,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
diff --git a/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h b/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
index 3f211182e..cb8a28c86 100644
--- a/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
+++ b/LUFA/Drivers/USB/Core/UC3/PipeStream_UC3.h
@@ -85,24 +85,24 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Discard_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
 			 *  }
 			 *  \endcode
-			 *
+			 *  
 			 *  <b>Partial Stream Transfers Example:</b>
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Discard_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -137,7 +137,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Null_Stream(512, NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -148,13 +148,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Null_Stream(512, &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -198,7 +198,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                        NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
@@ -211,14 +211,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                           &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -279,7 +279,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                       NULL)) != PIPE_RWSTREAM_NoError)
 			 *  {
@@ -292,14 +292,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Pipe_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                          &BytesProcessed)) == PIPE_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != PIPE_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
diff --git a/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h b/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
index 711d7a3a5..3269d2b1d 100644
--- a/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
+++ b/LUFA/Drivers/USB/Core/XMEGA/EndpointStream_XMEGA.h
@@ -87,7 +87,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Discard_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -98,13 +98,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Discard_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -140,7 +140,7 @@
 			 *  <b>Single Stream Transfer Example:</b>
 			 *  \code
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Null_Stream(512, NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *       // Stream failed to complete - check ErrorCode here
@@ -151,13 +151,13 @@
 			 *  \code
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Null_Stream(512, &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -199,7 +199,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                            NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -212,14 +212,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Write_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                               &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
@@ -276,7 +276,7 @@
 			 *  \code
 			 *  uint8_t DataStream[512];
 			 *  uint8_t ErrorCode;
-			 *
+			 *  
 			 *  if ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                           NULL)) != ENDPOINT_RWSTREAM_NoError)
 			 *  {
@@ -289,14 +289,14 @@
 			 *  uint8_t  DataStream[512];
 			 *  uint8_t  ErrorCode;
 			 *  uint16_t BytesProcessed;
-			 *
+			 *  
 			 *  BytesProcessed = 0;
 			 *  while ((ErrorCode = Endpoint_Read_Stream_LE(DataStream, sizeof(DataStream),
 			 *                                              &BytesProcessed)) == ENDPOINT_RWSTREAM_IncompleteTransfer)
 			 *  {
 			 *      // Stream not yet complete - do other actions here, abort if required
 			 *  }
-			 *
+			 *  
 			 *  if (ErrorCode != ENDPOINT_RWSTREAM_NoError)
 			 *  {
 			 *      // Stream failed to complete - check ErrorCode here
diff --git a/LUFA/Drivers/USB/USB.h b/LUFA/Drivers/USB/USB.h
index c99c1d267..626635c8d 100644
--- a/LUFA/Drivers/USB/USB.h
+++ b/LUFA/Drivers/USB/USB.h
@@ -189,7 +189,7 @@
  *  void EVENT_USB_Device_ConfigurationChanged(void)
  *  {
  *      LEDs_SetAllLEDs(LEDMASK_USB_READY);
- *
+ *      
  *      if (!(Audio_Device_ConfigureEndpoints(&My_Audio_Interface)))
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *  }
@@ -205,14 +205,14 @@
  *  int main(void)
  *  {
  *      SetupHardware();
- *
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_NOTREADY);
- *
+ *      
  *      for (;;)
  *      {
  *          if (USB_DeviceState != DEVICE_STATE_Configured)
  *            Create_And_Process_Samples();
- *
+ *          
  *          Audio_Device_USBTask(&My_Audio_Interface);
  *          USB_USBTask();
  *      }
@@ -293,30 +293,30 @@
  *  void EVENT_USB_Host_DeviceEnumerationComplete(void)
  *  {
  *      LEDs_SetAllLEDs(LEDMASK_USB_ENUMERATING);
- *  
+ *      
  *      uint16_t ConfigDescriptorSize;
  *      uint8_t  ConfigDescriptorData[512];
- *  
+ *      
  *      if (USB_Host_GetDeviceConfigDescriptor(1, &ConfigDescriptorSize, ConfigDescriptorData,
  *                                             sizeof(ConfigDescriptorData)) != HOST_GETCONFIG_Successful)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      if (MIDI_Host_ConfigurePipes(&Keyboard_MIDI_Interface,
  *                                   ConfigDescriptorSize, ConfigDescriptorData) != MIDI_ENUMERROR_NoError)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      if (USB_Host_SetDeviceConfiguration(1) != HOST_SENDCONTROL_Successful)
  *      {
  *          LEDs_SetAllLEDs(LEDMASK_USB_ERROR);
  *          return;
  *      }
- *  
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_READY);
  *  }
  *  \endcode
@@ -342,14 +342,14 @@
  *  int main(void)
  *  {
  *      SetupHardware();
- *
+ *      
  *      LEDs_SetAllLEDs(LEDMASK_USB_NOTREADY);
- *
+ *      
  *      for (;;)
  *      {
  *          if (USB_HostState != HOST_STATE_Configured)
  *              Create_And_Process_Samples();
- *
+ *          
  *          MIDI_Host_USBTask(&My_Audio_Interface);
  *          USB_USBTask();
  *      }
diff --git a/LUFA/Platform/UC3/ClockManagement.h b/LUFA/Platform/UC3/ClockManagement.h
index d0d8f71e8..2cd96d2ec 100644
--- a/LUFA/Platform/UC3/ClockManagement.h
+++ b/LUFA/Platform/UC3/ClockManagement.h
@@ -50,16 +50,16 @@
  *  Usage Example:
  *  \code
  *		#include <LUFA/Platform/UC3/ClockManagement.h>
- *
+ *      
  *		void main(void)
  *		{
  *			// Start the master external oscillator which will be used as the main clock reference
  *			AVR32CLK_StartExternalOscillator(0, EXOSC_MODE_8MHZ_OR_MORE, EXOSC_START_0CLK);
- *
+ *          
  *			// Start the PLL for the CPU clock, switch CPU to it
  *			AVR32CLK_StartPLL(0, CLOCK_SRC_OSC0, 12000000, F_CPU);
  *			AVR32CLK_SetCPUClockSource(CLOCK_SRC_PLL0, F_CPU);
- *
+ *          
  *			// Start the PLL for the USB Generic Clock module
  *			AVR32CLK_StartPLL(1, CLOCK_SRC_OSC0, 12000000, 48000000);
  *		}
diff --git a/LUFA/Platform/UC3/InterruptManagement.h b/LUFA/Platform/UC3/InterruptManagement.h
index 8dd1dc3d6..af99f0875 100644
--- a/LUFA/Platform/UC3/InterruptManagement.h
+++ b/LUFA/Platform/UC3/InterruptManagement.h
@@ -51,12 +51,12 @@
  *  Usage Example:
  *  \code
  *		#include <LUFA/Platform/UC3/InterruptManagement.h>
- *
+ *      
  *		ISR(USB_Group_IRQ_Handler)
  *		{
  *			// USB group handler code here
  *		}
- *
+ *      
  *		void main(void)
  *		{
  *			INTC_Init();
diff --git a/LUFA/Platform/XMEGA/ClockManagement.h b/LUFA/Platform/XMEGA/ClockManagement.h
index 9b3b56244..feef8898e 100644
--- a/LUFA/Platform/XMEGA/ClockManagement.h
+++ b/LUFA/Platform/XMEGA/ClockManagement.h
@@ -50,13 +50,13 @@
  *  Usage Example:
  *  \code
  *   	#include <LUFA/Platform/XMEGA/ClockManagement.h>
- *
+ *      
  *   	void main(void)
  *   	{
  *   		// Start the PLL to multiply the 2MHz RC oscillator to F_CPU and switch the CPU core to run from it
  *   		XMEGACLK_StartPLL(CLOCK_SRC_INT_RC2MHZ, 2000000, F_CPU);
  *   		XMEGACLK_SetCPUClockSource(CLOCK_SRC_PLL);
- *
+ *          
  *   		// Start the 32MHz internal RC oscillator and start the DFLL to increase it to F_USB using the USB SOF as a reference
  *   		XMEGACLK_StartInternalOscillator(CLOCK_SRC_INT_RC32MHZ);
  *   		XMEGACLK_StartDFLL(CLOCK_SRC_INT_RC32MHZ, DFLL_REF_INT_USBSOF, F_USB);
diff --git a/Projects/AVRISP-MKII/Doxygen.conf b/Projects/AVRISP-MKII/Doxygen.conf
index 12a6b9c78..24e139abe 100644
--- a/Projects/AVRISP-MKII/Doxygen.conf
+++ b/Projects/AVRISP-MKII/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "AVRISP-MKII Clone Programmer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Benito/Doxygen.conf b/Projects/Benito/Doxygen.conf
index 44ff2a40c..64e72a1a7 100644
--- a/Projects/Benito/Doxygen.conf
+++ b/Projects/Benito/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Benito Arduino Programmer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/HIDReportViewer/Doxygen.conf b/Projects/HIDReportViewer/Doxygen.conf
index b792c67bd..4906ca5ea 100644
--- a/Projects/HIDReportViewer/Doxygen.conf
+++ b/Projects/HIDReportViewer/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "HID Device Report Viewer Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/LEDNotifier/Doxygen.conf b/Projects/LEDNotifier/Doxygen.conf
index 562fcd8a8..61467471f 100644
--- a/Projects/LEDNotifier/Doxygen.conf
+++ b/Projects/LEDNotifier/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - USB LED Notifier Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -963,12 +957,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -977,6 +965,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1134,7 +1133,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1155,11 +1154,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1728,7 +1722,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MIDIToneGenerator/Doxygen.conf b/Projects/MIDIToneGenerator/Doxygen.conf
index 50223a882..277c61599 100644
--- a/Projects/MIDIToneGenerator/Doxygen.conf
+++ b/Projects/MIDIToneGenerator/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - MIDI Tone Generator Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Magstripe/Doxygen.conf b/Projects/Magstripe/Doxygen.conf
index 5bde2d854..aaddc869c 100644
--- a/Projects/Magstripe/Doxygen.conf
+++ b/Projects/Magstripe/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Denver Gingerich's Stripe Snoop Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MediaController/Doxygen.conf b/Projects/MediaController/Doxygen.conf
index 4ef61870d..32c532d93 100644
--- a/Projects/MediaController/Doxygen.conf
+++ b/Projects/MediaController/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - Media Controller Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/MissileLauncher/Doxygen.conf b/Projects/MissileLauncher/Doxygen.conf
index 480832870..512649dfe 100644
--- a/Projects/MissileLauncher/Doxygen.conf
+++ b/Projects/MissileLauncher/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Dave Fletcher's Missile Launcher Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/RelayBoard/Doxygen.conf b/Projects/RelayBoard/Doxygen.conf
index 03778cb8f..dc116f0cf 100644
--- a/Projects/RelayBoard/Doxygen.conf
+++ b/Projects/RelayBoard/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "OB's Dual-Relay Outlet Control Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/SerialToLCD/Doxygen.conf b/Projects/SerialToLCD/Doxygen.conf
index eaa8e1688..b16a3b8a8 100644
--- a/Projects/SerialToLCD/Doxygen.conf
+++ b/Projects/SerialToLCD/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Simon Foster's USB Serial to HD44780 LCD Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/TempDataLogger/Doxygen.conf b/Projects/TempDataLogger/Doxygen.conf
index 7a3832194..70f6e0aeb 100644
--- a/Projects/TempDataLogger/Doxygen.conf
+++ b/Projects/TempDataLogger/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "Temperature Datalogger Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/USBtoSerial/Doxygen.conf b/Projects/USBtoSerial/Doxygen.conf
index 57f8a9a67..ae0ed4822 100644
--- a/Projects/USBtoSerial/Doxygen.conf
+++ b/Projects/USBtoSerial/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - USB to Serial Device Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/Webserver/Doxygen.conf b/Projects/Webserver/Doxygen.conf
index 691ce6a79..3d431fd09 100644
--- a/Projects/Webserver/Doxygen.conf
+++ b/Projects/Webserver/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - uIP Powered Webserver Project"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -961,12 +955,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -975,6 +963,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1132,7 +1131,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1153,11 +1152,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1726,7 +1720,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
diff --git a/Projects/XPLAINBridge/Doxygen.conf b/Projects/XPLAINBridge/Doxygen.conf
index 2e5c3a3c2..827d892c6 100644
--- a/Projects/XPLAINBridge/Doxygen.conf
+++ b/Projects/XPLAINBridge/Doxygen.conf
@@ -1,4 +1,4 @@
-# Doxyfile 1.8.0
+# Doxyfile 1.8.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -32,7 +32,7 @@ PROJECT_NAME           = "LUFA Library - XPLAIN Serial Bridge/PDI Programmer Pro
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer
@@ -563,12 +563,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = YES
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -960,12 +954,6 @@ HTML_COLORSTYLE_GAMMA  = 80
 
 HTML_TIMESTAMP         = NO
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
@@ -974,6 +962,17 @@ HTML_ALIGN_MEMBERS     = YES
 
 HTML_DYNAMIC_SECTIONS  = YES
 
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
@@ -1131,7 +1130,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX       = YES
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1152,11 +1151,6 @@ GENERATE_TREEVIEW      = YES
 
 ENUM_VALUES_PER_LINE   = 1
 
-# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list.
-
-USE_INLINE_TREES       = NO
-
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
@@ -1725,7 +1719,7 @@ CALLER_GRAPH           = NO
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
-- 
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