Fix auto-close in a repo with missing commits in Phabricator db

Summary:
After adding more error logging: https://secure.phabricator.com/differential/diff/5295/, discover.php prints the output: https://secure.phabricator.com/P427

The problem is that there are gaps in the commits and revisions in Phabricator's DB for the repo. For some git commits, both the phabricator commits and the differential revision are missing (because of a mysterious DB data loss. nharper should be able to recover it); for some other git commits, the phabricator commits are missing (probably also because of the daba loss mentioned above). This can also happen if the git commits were too big to be parsed by phabricator.

Because of the gap, the pull daemon detects them as new autoclose commits on the branch

(https://secure.phabricator.com/diffusion/P/browse/master/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php;382bafa271ec4962$267)
(https://secure.phabricator.com/diffusion/P/browse/master/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php;382bafa271ec4962$592)

Then tries to update it

(https://secure.phabricator.com/diffusion/P/browse/master/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php;382bafa271ec4962$616)

and will fail because the commit doesn't exist in the DB.

(https://secure.phabricator.com/diffusion/P/browse/master/src/applications/repository/daemon/PhabricatorRepositoryPullLocalDaemon.php;382bafa271ec4962$341)

After the exception is thrown, all the commits just detected are not marked as 'seenOnBranches', so they won't be marked as closed by the CommitMessageParserWorker.

This also explains the weird behavior where the parsing of the commits is always paused for 15 minutes and then gets started again. The parsing pauses because the process listed at https://secure.phabricator.com/P427 takes quite some time to finish before it can record tha tasks. The parsing happens all the time because the process will be executed again and again.

A better fix might be to put all the missing commits in the repository_badcommit table and check against it.

Test Plan: will run 'discover.php FBCODE' to test it.

Reviewers: epriestley, vrana

Reviewed By: vrana

CC: nh, vrana, aran, Korvin

Differential Revision: https://secure.phabricator.com/D2846