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.

Initial move and rename of database classes to PSR-0 namespaces.  So far only MySQL has been converted.