Global file mode override now works properly with the file mode stored in the tree node.
Renamed git_checkout_index to what it really was, and removed duplicate code from clone.c. Added git_checkout_ref, which updates HEAD and hands off to git_checkout_head. Added tests for the options the caller can pass to git_checkout_*.
Includes unfinished win32 implementation.
Removed the BUILD_CLAR CMake flag, and updated the readme.