Uninstall Messages from the extension instead of using the AppManager.

This fixes a failure to uninstall when the app was originally installed
with a query parameter.

Bug: 946319
Change-Id: I06c4051cdeed6626119332524bf8cd5abfe0c836
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/1549211
Reviewed-by: Azeem Arshad <azeemarshad@chromium.org>
Reviewed-by: Kyle Horimoto <khorimoto@chromium.org>
Commit-Queue: Jon Mann <jonmann@chromium.org>
Cr-Commit-Position: refs/heads/master@{#647581}