pass --git-dir, rather than changing cwd

pass --git-dir, rather than changing cwd

If .git is a gitlink file, setting cwd to it will fail, but --git-dir
will succeed. And this is the only place where it sets cwd when running
git, everywhere else already uses --git-dir.

Note that, git-annex's submodule fixup code usually converts gitlink
files to symlinks, so this wasn't usually problem. Still, worth fixing.

This commit was sponsored by Svenne Krap on Patreon.