Clean My Mac cleared .h files?

Ive been wracking my brains for the last couple of hours as to why my arduino sketches wouldnt accept any libraries. When importing them via the sketch menu, the #include <lib.h> file didnt appear. I finally got round to examining the libraries directly (after a few more long winded ideas of what could be wrong) and discovered all the .h files were missing.

I did a “clean my mac” run this morning, and was wondering if that might have caused it? Has anyone come across this before? Alternatively, I also ran this script>

to uninstall some frameworks too. Could the ardunio have been sharing anything with this?