Restore previous behavior and keep emitting a warning when an existing
gclient entry is not longer part of the client. Additionally, suggest
the usage of `gclient sync -D` to automatically remove them.

Change-Id: I62d4662ae4d0886d340230019419b68debffc5ba
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/1483031Reviewed-by: Dirk Pranke <dpranke@chromium.org>
Reviewed-by: Michael Moss <mmoss@chromium.org>
Commit-Queue: Henrique Ferreiro <hferreiro@igalia.com>