I put a bug in one of my packages that kept atom from starting. So I started Atom in safe mode. When I brought up the settings tab and clicked on Packages I saw my installed packages but when I clicked on a package name nothing happened. Also there was an install button next to each one that makes no sense in safe mode.
I brought up help for APM and to my surprise there is no APM disable command.
I will move my bad package out of my packages directory to work around this but a lot of what I described above doesn’t smell right.