Something to consider - this isn't from your current version, but the original, and I'm guessing the relevant parts of the code are the same in both:
I just reflashed my FIASCO image. I had never had a chance to disable or uninstall ApMeFo before I got my N900 into the boot-loop that made reflashing necessary. However, I noticed that upon booting up after the FIASCO reflash, all of my folders are still there. (I'm pretty sure this is both expected, and probably not problematic, though.)
I have not started reinstalling anything yet, ApMeFo included. However, this leads us to the following point: is there any possibility that ApMeFo, when installed on a system that already has a bunch of menu folders, will glitch somehow? My guess is no, but I figured it was worth mentioning, and if it does turn out to be the case whenever I get around to installing ApMeFo again, I'll let you know.
@Mentalist Traceur - ApMeFo generated files are stored in /home/ partition so does not vanish after reflash.
Yes, I deduced that. I was wondering if those left-over generated files would conflict with the next install of ApMeFo, or if the reinstalled ApMeFo will just read them as its own. (Then I typed-out my guess that this was most likely the case, but I wasn't completely certain.)