bot_update doesn't properly cleanup git index state from unmerged paths,
which are likely if Rietveld patches were failed to be applied in prior
runs in the same checkout dir.

R=machenbach@chromium.org
BUG=692067

Change-Id: I8fd326caefce8623731697a368cbad3159405257
Reviewed-on: https://chromium-review.googlesource.com/442426
Commit-Queue: Andrii Shyshkalov <tandrii@chromium.org>
Reviewed-by: Michael Achenbach <machenbach@chromium.org>