Moved code around and deleted duplicated and unused code.

Moved code around and deleted duplicated and unused code.

 - Moved down SourceCell and SourceController to match master.
 - Moved down InstalledController to be in a sane location.
 - Merged DepSubstrate() in with Confirmation Controller's section to avoid a useless and mis-named section.
 - Removed CY prefix on a number of classes where it does not belong.
 - Changed a few folding markers to have more descriptive and accurate names.
 - Probably more.