General refactoring

Refactor structure of plugin
- Main logic begins in clef-require.php
- wpclef.php maintains constant indicating whether Clef is the base plugin
- Classes no longer inherit from ClefBase, which was becoming a repository for random functions
- Classes now implemented as singletons rather than static classes
- Plugin-setup related functions now in separate class, ClefSetup
- Site options/settings access now encapsulated in separate class, ClefInternalSettings
- Admin menu only rendered when Clef is base plugin
- Activation/uninstall hooks only registered when Clef is base plugin
- Several unused functions have been removed