I just installed the atom snap package mentioned here:
After installing the snap (and confirming that worked) I removed the atom deb package.
Now I have an issue with the icon. The atom icon shows up when searching for atom in the dash (Unity) and I can select it.
It then pops up in the launcher as well, but is then followed by an ? icon. The ? icon then actually points to the atom window, and after atom is fully launched, the atom icon goes away and I am left with only the ? icon.
I can pin the atom icon, and if I click it, it will start atom, but again the ? icon will pop up and be connected to the atom window.
I tested this on a clean (VM) of Ubuntu 16.04 and can’t reproduce it. I installed the snap, then ran it from the dash. I know in the past (pre-snaps) Unity (or BAMF) would get its pants in a bunch about icons and sometimes do this (or similar behaviour) which is often un-wedged with a desktop logout/login cycle. Does that work around it for you?
The issue is gone here now as well, after I restarted.
(My docking station was delivered) So I guess logging out and in again would have solved the issue as well.
I think it was still pointing to the deb icon, and that only was refreshed after logging in again.