ouch The removal of stray files and the cleaning of the Crysis build are 2 separate procedures which really have nothing to do with each other.
The first one has to be mandatory, it cleans MWLL mod folder. This is because some of the files there may actually trigger the cheat protection. Disabling the first procedure is not a thing we want to do, cause we want to make sure that a user is always able to start the game without any issue.
If you get a notification everytime, it means that in your MWLL mod folder there are unnecessary files that are not supposed to be there, so you should either move or delete them.
Cleaning Crysis build is another thing. As stated, is designed for mappers, because sometimes, by using the editor, you end up having stuff saved in the Crysis installation, which makes it available in the editor for you, but not in game for anyone else. By cleaning Crysis build, you can make sure this doesn't happen.