Added new doxygen_upgrade and doxygen_create targets to the DOXYGEN build system module. Clean up CORE build system module.

Document build system targets. Add a rule to the BUILD module that is run if a source file does not exist to show an error to the user, rather than running the check-source rule before each build (slightly faster/more portable and the generated error is then a true make error).

Rename build system module makefiles from "lufa.MODULE.in" to "lufa_MODULE.mk" to prevent makefile from assuming the include is an old style build rule, slowing down the build process.

Prevent the BUILD module from shell-executing multiple processes to determine the avr-size flags to speed up the build, unless the size rule is invoked.

Add warnings and set warnings as errors to the SingleUSBModeTest build test makefile.

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

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.

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

Disable inbuilt make rules in the LUFA build system for speedups when compiling many projects recursively.

Add .PHONY targets in all build system modules. Alter BUILD module so that the existence of source files are checked before the build is started.

Rename program_ee AVRDUDE module target to program-ee. Update CORE build module to print out lists one item per line, rather than all on one line.

Clean up CORE build system module, use simple rather than recursive make variables for internal constants and $(shell) derived values.

Remove any variables in the optional build variable list that are marked as mandatory by one or more included build system modules in the CORE build system module. Alter DOXYGEN build system module to by default override the Doxygen configuration file stylesheet and replace it with the LUFA Doxygen stylesheet.