Updated Xcode project for reorganized structure

Also updated include paths.
[CMake] Box2d and Chipmunk now working on Linux.
Removed extraneous build schemes from version control
Fixed iOS build after project reorganization

Many include paths changed, some were added, some USFoo references became ZLFoo
Merge branch 'master' of github.com:moai/moai-dev
Merge remote-tracking branch 'upstream/master'