Fix breakage when git is configured with safe.bareRepository = explicit

Fix breakage when git is configured with safe.bareRepository = explicit

Running git config --list inside .git then fails, so better to only
do that when --git-dir was specified explicitly. Otherwise, when the
repository is not bare, run the command inside the working tree.

Also make init detect when the uuid it just set cannot be read and fail
with an error, in case git changes something that breaks this later.

I still don't actually understand why git-annex add/assist -J2 was
affected but -J1 was not. But I did show that it was skipping writing to
the location log, because the uuid was NoUUID.

Sponsored-by: Graham Spencer on Patreon