The current "merge" checkout strategy is unsafe. It merges the PR and the base
branch without holding the directory lock(s), so there is a potentially
very long window where another PR can be applied and be unexpectedly reverted
later.

This happens occasionally if a PR causes plans in multiple directories, but
is almost _guaranteed_ to happen if the initial plan has to wait until a
lock is freed up and a manual "atlantis plan" command is given.

Instead of printing a warning when this happens, we now merge again
if necessary while holding the lock. Plans are then guaranteed to only
be made when merged with the base branch for each directory being planned,
and applying later should be safe even if the base branch sees further
updates.

This fixes/affects runatlantis#804, runatlantis#867, runatlantis#979

We now verify that the first Clone with CheckoutMerge=true with
a diverged base branch atually clones and merges again.