Added Doxygen support

Output folder is ignored by Git
Documented most of upgrade_type
Doxygen now outputs private, static, etc
Documented most of upgrade.h
No more warnings for undocumented code
Added namespace and file comments

Namespaces Glest and Game are now commented. To avoid unnecessary
duplication, they're only commented in one place (main.cpp).
Merge pull request #20 from MikeHoffert/documentation

Documentation is always a good thing