There as been a lot of shuffling behind the scenes. Everything should work as before, with some much needed fixes, and the AtomProbeLab folder looks a lot cleaner. All of the m-files which make up APL have been moved into a folder called "/src", so when you want to use them simply add:
addpath('src\');
to your script and you will be able to access the goodies within.
Stay tuned for a big release with a bulk peak overlap solving function coming soon!