Replace C style comments in assembly code with true assembly comments for consistency and to prevent it from confusing syntax highlighters.

Modify CDC and DFU bootloaders so that the various BootloaderAPI components are in unique sections and mapped explicitly - this will ensure the API and signature entries are always linked at the correct explicit address.

Add missing <math.h> include for the UC3 devices, hide CDC class driver stream functions for unsupported platforms.

Add ability to generate SYM files in the BUILD module. Clean up build system output to be slightly more human readable.

Add checks to the endpoint and pipe configure functions and fail if the requested endpoint or pipe number is above the maximum for that device.

Add OBJDIR optional build variable to the BULD build system module, to allow the user project to relocate the output object and dependency files to a different directory.

Make sure the main library core makefile does not interfere with the Doxygen module configuration if included in a legacy makefile.

Update CORE build system module to convert the sorted module data lists into printable lists, substituting in a "(None)" entry when no data is available.

Add Build System documentation to the library manual. Update CPPCHECK build system module so that it uses the SRC variable rather than just the project directory.

Change the build system build module makefiles to have a set of sanity check macros they can call to verify user data. Add additional sanity checks.

Added new JTAG_ENABLE() macro for the AVR8 architecture. Fixed the JTAG_DISABLE() macro clearing all other bits in MCUSR when called.

Moved the XPLAIN board specific bootloader entry condition code to the Application_Jump_Check() function of the DFU bootloader, added support for the original XPLAIN board to the CDC class bootloader.

Fix BUILD module so that user flags are applied after all auto-generated flags, ensure dependency files are generated with a .d extension rather than a .o.d extension, allow use of full part names ("at32uc3a0256") instead of GCC truncted part names ("uc3a0256").

Simplify AVRDUDE build module, ensure that the correct target names for FLASH and EEPROM writing are passed to the programmer tool.

Add optional CPPCHECK_FLAGS parameter to the CPPCHECK build module, for miscellaneous user flags. Ensure the user flags are applied after all auto-generated flags.

Strip out BuildTest sub-makefile contents as much as possible. Remove old UC3 build test makefile from the ModuleTest build test. Add platform module to the example LUFA makefile.

Add new ATPROGRAM build system module. Add ATPROGRAM and CPPCHECK modules to all application makefiles.

Add symbol-sizes target to the BUILD build system module to print a size-sorted list of symbols from a compiled application, in decimal bytes.