Ref T4365. Primary search currently uses PhabricatorSearchQuery for storage, which is pretty much the same as PhabricatorSavedQuery, except that it's old and not used anywhere else anymore.
Maniphest used to also use this table, but no longer does after Septmeber, 2013. We need to retain the class so the migration can work.
This introduces PhabricatorSearchApplicationSearchEngine and PhabricatorSearchDocumentQuery, but they're both stubs that I just needed for technical reasons and/or to pass lint. The next couple patches will move logic into them and use ApplicationSearch properly.