Add prune-safety to StGIT

The top of each patch will also be stored in the .git/refs/patches/branch/
directory so that tools commands like git prune would not destroy the
unapplied patches. Since there is no support for patch history at the
moment, a git prune command would remove all the previous versions of a
patch (which were no longer accessible anyway).

The old repositories are automatically upgraded.

Signed-off-by: Catalin Marinas <catalin.marinas@gmail.com>