When upgrading this install, I hit this problem when applying the xhpast rename:
>>> [10] <query> RENAME TABLE secure_xhpastview.xhpastview_parsetree TO secure_xhpast.xhpast_parsetree <<< [10] <query> 3,472 us [2015-11-16 16:45:15] EXCEPTION: (AphrontQueryException) #7: Error on rename of './secure_xhpastview/xhpastview_parsetree.frm' to './secure_xhpast/xhpast_parsetree.frm' (Errcode: 2) at [<phutil>/src/aphront/storage/connection/mysql/AphrontBaseMySQLDatabaseConnection.php:311]
That's failing because the xhpast database does not exist. It doesn't exist because Phabricator believes it already exists, so it does not recreate it:
$ ./bin/storage status ... phabricator:db.xhpast Applied - db xhpast ....
The date of the patch application is October, 2012:
mysql> select FROM_UNIXTIME(1349752436); +---------------------------+ | FROM_UNIXTIME(1349752436) | +---------------------------+ | 2012-10-09 03:13:56 | +---------------------------+ 1 row in set (0.00 sec)
Modern quickstart.sql does not reference this database. I don't recall what happened with in 2012. We might be fine (whatever happened might be unique to this install) but there may be a more widespread issue here.