Handle missing plugins during sql-upgrade, refs #4557

Squashed commit of the following:

commit 4dd19568860d1787af09cba5103d80c62e3225a5
Author: Mike Gale <mikeg@artefactual.com>
Date:   Mon Sep 15 13:20:09 2014 -0700

    Simplify removing plugins and choosing new theme

    - Now prompts the user to remove plugins and
      whether or not to choose a new theme.

    - Disabled automatically inserting dominion as the
      theme in arMigration0095.class.php.

commit 69726022eec4c8565fc2e2a34336c4807977caa1
Author: Mike Gale <mikeg@artefactual.com>
Date:   Sun Aug 31 00:26:36 2014 -0700

    After theme change, check for missing plugins.

    - After checking for missing theme & choosing a new one,
      this code will check for missing plugins in general and
      remove them from the settings table in the database,
      if they aren't present on the filesystem.

    Remove debugging dummy elements

    remove debugging plugin name

    Remove useless setValue call from debug

    Remove extra settings get

commit 5224aeeead36a617d8ccbac374b0327059e5869b
Author: Mike Gale <mikeg@artefactual.com>
Date:   Sat Aug 30 22:58:21 2014 -0700

    Ask user for new theme if missing issue #4557