Issue #1392754 by tss, justAChris, jhodgdon: Comply with new documentation standards for @file for namespaced class files

Issue #1614186 by RobLoach, tim.plunkett, msonnabaum, Crell, jhodgdon, Niklas Fiekas: Update coding standards for using 'native' PHP classes like stdClass in namespaced code.

Rename classes to remove the redundant Database prefix and move query exceptions into the query namespace.