@hedefalk ok, so I think I may have just fixed it. Here is what I did:
1 - git cloned ensime-atom directly into the ~/.atom/packages folder
2 - start up atom, you will see on the lower right a little red button, click on it and you get a screen showing incompatible packages. On that screen, you will see an ill-placed button that says “Rebuild Packages”. Click that button and Atom does its thing. This is in Atom Editor itself, not on the command line.
3 - After rebuild, you get an option to say “Reload”, click on that to reload ensile.
4 - Get some green notifcations that all is well. I know have ensime available!