Lets say we detect Cygwin as the FS type, because cygpath appeared in the user's $PATH.

But the user has configured SmartGit to *not* use Cygwin.

Now when JGit tries to use an SSH connection, its going to be asking the user's *Cygwin* home directory for the .ssh/config and their SSH keys.  But that makes no sense, if SmartGit was configured to *not* use Cygwin, why is it using the Cygwin based settings?

So, this needs to be using the same FS instance that the Repository its being called by is using.