Change Doxygen configuration files to not produce 4096 directories for the documentation files -- the LUFA components do not generate enough documentation files to justify the large performance hit of creating so many directories.

Fix missing Doxygen documentation in the Class Driver Mass Storage Device demo.

Added new EEPROM and FLASH buffer versions of the Endpoint and Pipe stream functions. Changed Endpoint.c and Pipe.c to use a templated system to build the seperate functions, rather than duplicating each function's code many times.