Fixed some compiler warnings.
Changes due to libgit2 update.

Libgit2 used now on development branch, commit
901c34f233cf49c75a1fa9a4a7e97cfe5b87269e.
Switched development to MSVC 2013.

Updated instructions and build settings to reflect this. Also using the
Boost SVN r86365, since neither the 1.54 release nor the 1.55 beta want
to build using MSVC 2013.
A bunch of file permissions changes, I think.

Not sure why Git is seeing the files as being changed.