Protect Ships/VAB and Ships/SPH from deletion.

This close #666 by not allowing theses two directory to be erased.
This also protect from the Exception raised when trying to write to a deleted directory by rethrowing a DirectoryNotFoundKraken catched in CmdLine and GUI.

Maybe there should be a more generic way to exclude a directory from deletion, but I can't think of other right now.

I think removing Ships folder should not be supported as it cause an DirectoryNotFoundException in-game (in sandbox or in career with the "Allow Stock Vessels" option), so I think it should close #582 too.