init: add multi-manifest support

This moves more of the manifest project handling into ManifestProject.

Change-Id: Iecdafbec18cccdfd8e625753c3bd1bcddf2b227f
Reviewed-on: https://gerrit-review.googlesource.com/c/git-repo/+/334520
Tested-by: LaMont Jones <lamontjones@google.com>
Reviewed-by: Mike Frysinger <vapier@google.com>