Removes deprecated patch_project_roots in bot_update,
and the TODOs used for migration.

Depends: https://codereview.chromium.org/1913863002

R=phajdan.jr@chromium.org,machenbach@chromium.org
BUG=605563

Review URL: https://codereview.chromium.org/1920933002

git-svn-id: svn://svn.chromium.org/chrome/trunk/tools/depot_tools@300153 0039d316-1c4b-4281-b951-d872f2087c98