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I use Cygwin on Windows 7 and found that the default symlinks don't allow Git or Phpstorm to work properly with modman'd projects.
The problem is resolved by setting 'winsymlinks:native' in the CYGWIN environment variable.
Apparently, command line PHP on Cygwin uses this variable for its "symlink" and related functions.
My fork fixes a number of things, but this is the main item.