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).

Upgrade Doxygen configuration files, custom style CSS and DOXYGEN build module for the latest Doxygen release.

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.

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.

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

Add explicit blank checks in the build system for user-set but blank variables that must not be blank.

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.

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.

Add EEPROM programming target to the AVRDUDE build system module. Correct message output test for the BUILD build system module. Clean up DOXYGEN build system module logic.