Revert "pass --git-dir, rather than changing cwd"

Revert "pass --git-dir, rather than changing cwd"

This reverts commit c142696c587100b195accec4e9bfaa26cde73d48.

It turns out it was not needed; 681313dfd4e840e6366f3c39eddd92f65d764188
fixed up the git dir, so setting cwd to it works ok.

But worst, this commit broke the test suite massively. I don't understand how.
git-annex get was failing. Very weirdly, git-annex find in a fresh
clone of an annex repo, during autoinit, was displaying a side message
-- but side messages are disabled when running find.