Remove deprecation warning about registry plugin

[alechirsch]

This removes the deprecation notice:

Registry plugin was moved into core Bookshelf. You can now register models using `bookshelf.model()` and collections using `bookshelf.collection()` without having to call `.plugin('registry')`. Remove any `.plugin('registry')` calls to clear this message.

It also fixes deprecations for createTableIfNotExists in knex, and findWhere in bookshelf.

I tried to run the tests with upgraded bookshelf and knex versions, however one of the tests failed and I spent way too much time trying to figure out what was causing it.

[alechirsch]

@blah238 Would you be able to get this through?