When source repo is a 'shallow clone', `.git/shallow` is not linked to
the new workdir. Which makes running git command fails in new workdir.

Change-Id: I81d38b7b2cccc482711dcc1dd02ea06fbd01a56d
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/2211635Reviewed-by: Aaron Gable <agable@chromium.org>
Commit-Queue: Richard He <linyhe@microsoft.com>