There should be a contradiction in the place in the preferences, where it says 'clear cache' -- the two file save locations -- one is the file location of the .cpt file, and the other is the cache file location. these should NOT be the same, nor should it be an option to be saved in the same place.

Why you ask?
Because I had my HUGE module saved to the same location in both of these locations. I cleared my cache. Then... POOF, my entire module - GONE!. Up in smoke. Disappeared.

Nothing told me I was deleting my entire module. Nothing warned me. Just 1 click, and its gone.

Recommendation:
-make it a contradiction so that people cannot save their .cpt file in the same file location as the cache folder
-make it not possible to delete the project while clearing the cache.
-implying that 'clear cache' is doing much more than just clearing cache, which is a normal every day thing we do to make things run smoother.