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OS X spawns from two different cultures: Unix/POSIX and Mac OS. Folders like /usr, /var, /etc, the command line shell in the Terminal (bash by default) all belong to POSIX environment. Portable software targeting Unix-based systems (like git) go into /usr/local by default, or into package manager's defined location if installed by it (Homebrew uses ...
This might be good reading material for all your questions. OS X Mavericks Core Technologies Overview October 2013 http://www.apple.com/media/us/osx/2013/docs/OSX_Mavericks_Core_Technology_Overview.pdf
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