Hi guys,
A few weeks ago I had a real problem organizing my Arduino code for github. I struggled with an inability to put arduino libraries in a subfolder within the Libraries directory. It's not as simple as include "folder/lib.h". Long story short, what seems to make the most sense right now is to clone my entire Arduino folder into Arduino2, then go to Arduino > Preferences > Sketchbook Location, and pointing to that new folder instead.
I've done this, and my code seems to compile, find the libraries correctly, etc. I just wanted to double check that there wasn't anything I was missing, and this should be a fine way to create a separate Arduino workspace for a separate set of sketches and Libraries (in this case, for my work).
Thanks!