I can give some input here:
I tested AIOWPS on ClassicPress.
I first installed ClassicPress Alpha version, installed this plugin, and set a few settings, initialised the file change scanner, etc. All was fine except that it said I was running Windows (I did the tests on a Mac running XAMPP) so I couldn’t access the File Permissions screen.
Then I overwrote the Alpha installation with the Beta version, and all was still fine. The manual file scanner of AIOWPS showed a large number of changed files, which is to be expected, and all other functions still looked fine, with the exception of the File Permissions screen as before.