The implementation of AlphaPeptDeep support in PR#3123 currently puts run artifacts in Skyline.exe/Tools/alphapeptdeep/<data-time-stamp>/*

This needs to go somewhere else. I would suggest that that alphapeptdeep/<data-time-stamp>/* just go into the same folder the final .blib file is going into. The files seem of interest to the user. They are extremely unlikely to find them in the Skyline.exe/Tools folder which may be buried deep in the <user>/AppData folder which is hidden by default. If we wanted them to be that hidden but still findable, they should go into a temporary folder, but these methods will often end up creating cruft that builds up over time without the user being aware of what is going on.