sync: Refresh index before updating repo

If the repo index is stale, reset --keep will refuse to reset workspace.
An index can be stale if there are any modifications to file node,
including mtime, atime, ownership changes, etc.

Bug: b/375423099
Change-Id: Ibef03d9d8d2babbb107041707281687342ab7a77
Reviewed-on: https://gerrit-review.googlesource.com/c/git-repo/+/460022


Commit-Queue: Josip Sokcevic <sokcevic@chromium.org>
Tested-by: Josip Sokcevic <sokcevic@chromium.org>
Reviewed-by: Scott Lee <ddoman@google.com>