RepoCommand: Copy manifest upstream into .gitmodules ref field

RepoCommand: Copy manifest upstream into .gitmodules ref field

Project entries in the manifest with a specific sha1 as revision can
use the "upstream" field to report the ref pointing to that sha1. This
information is very valuable for downstream tools, as they can limit
their search for a blob to the relevant ref, but it gets lost in the
translation to .gitmodules.

Save the value of the upstream field when available/relevant in the
ref field of the .gitmodules entry.

Change-Id: I14a2395925618d5e6b34be85466e32f5ef8fbf6e