[Core] Remove Database::singleton function

[driusan]

There are currently 3 methods of getting a reference to a database in LORIS, in order of preference:

1. LorisInstance->getDatabaseConnection()
2. NDB_Factory::singleton()->database();
3. Database::singleton()

The only reference to 3 left is in the implementation of option 2. This removes the Database::singleton by inlineing the reference into the factory and removes all remaining references to Database::singleton (mostly from documentation and a couple unit tests.)

[ridz1208]

looks good other than the couple comments

[driusan]

@kongtiaowang it seems like some unit tests can't connect to the database but the log has the credentials and it's consistently the same tests.. do you have any ideas?

[driusan]

@ridz1208 getting the tests to pass took more significant changes than expected, can you re-review?

old review