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Huh, a bunch of us at Canonical use Atom with Unity, I think you might be missing the .desktop file if you're pulling it from github? Make sure you have one for atom in /usr/share/applications. I took a quick scan of the github repo and didn't see one, so you might want to just grab the .desktop and icon from the PPA package.

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I've used atom since it was open sourced and really like many of the features it offers. But there is an issue with the mouse cursor disappearing when hitting the ALT key described here https://github.com/atom/atom/issues/2122 and the launch problem https://github.com/atom/atom/issues/3190

I've never used a .desktop file for atom and had no problems launching it until a recent update from the master repo. Guess I'll try installing the PPA package to see if that works.

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