This is in keeping with git's default behavior for other porcelain
commands. It also makes it more tenable for projects to introduce
submodules instead of repo manifests without breaking git-cl upload
and similar tools.

Bug: 958499
Test: Run locally
Change-Id: Id9595271bf89aa8ba928026501a4c9487e5abf8e
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/1592572Reviewed-by: Aaron Gable <agable@chromium.org>
Reviewed-by: Dirk Pranke <dpranke@chromium.org>
Commit-Queue: Eli Ribble <eliribble@chromium.org>