manifest_xml: skip config lookup during first init

Trying to use the config state when the git tree hasn't yet been
created hits bad side effects.  Add a check to avoid probing the
config logic during the first run.  It's not clear what's going
wrong at the lower layers, but this gets us back to the behavior
before we added worktree support, so lets settle the status quo.

Bug: https://crbug.com/gerrit/12387
Change-Id: I85b56797455f3c2e249d02c18496e060be05501d
Reviewed-on: https://gerrit-review.googlesource.com/c/git-repo/+/256592
Reviewed-by: Xin Li <delphij@google.com>
Reviewed-by: Mike Frysinger <vapier@google.com>
Tested-by: Mike Frysinger <vapier@google.com>