Make modules toggleable on/off

[ExpiredPopsicle]

Make it so it's easy to turn the effects of modules on and off at runtime.

This implementation should work like this:

• Per-module on/off flag
• Skip _process calls (from the main app) on modules that are disabled
• Sync scene_init and scene_shutdown calls with module activation/deactivation
• Fixup existing scene_init/scene_shutdown calls in the main app to be aware of module activation status