Added a whole lot of documentation comments.

I also fixed a couple of references to exception classes in the global
namespace, and adjusted the existing PHP Doc as necessary.
Renamed instance variable so it matches what's actually being used.

This was a bad copy+paste job.
Created standard function to get the filename of a persisted cache object.
Renamed constant.

Also removed an old parameter that was removed in a call to saveData()
on the Cache class.
Made it optional to use the cache when initialsiing the config tree.