Modify default Homebrew installation directory to /usr/local
Use Homebrew recommended installation command and run brew doctor

This command also takes care of setting the permissions on the /usr/local/
folder so that we don't have to care about this. During initial clenaup,
remove contents of /usr/local without removing the folder (may not be
permitted).
Do not allow BREW_DIR to be overriden

Since using the default Homebrew installation command, we don't have the
choice of the installation directory anymore.
Clean Homebrew as suggested in the installation command
Test if git is already installed
Prepend /usr/local/bin to the path before running brew/doctor
Install scc Python dependencies
Install Homebrew Bio-Formats
Remove taps during Homebrew cleanup
Allow to specify different default directory for Homebrew

Note that neither the cleanup nor the installation will currently work is the Homebrew directory is different from /usr/local
Use word boundary when looking for Homebrew installed git
Merge pull request #733 from sbesson/rebased/develop/homebrew_folder

Modify default Homebrew installation directory to /usr/local (rebased onto develop)