I’ve just been trying to find someone else with this experience, as it’s just happened to me. I was editing a file, and hit a short cut (clearly the wrong one, though I don’t know what exactly I hit). All of the files in the sidebar went orange. I didn’t know what that was, and suspected I’d toggled some selection state (I’m new to Atom). So I restarted Atom, and the project was gone.
No big deal I thought, I tabbed to Tower (my Git client of choice) and went to reset changes to last commit, as I had two days of development on this project all committed to my develop branch, though hadn’t yet pushed it anywhere…huge mistake in retrospect. Oddly, no changes in working copy. I went to view the commit history and it was empty. I went to finder, and the entire project has been deleted.
Again, no big deal I thought. I went to Trash. Nothing… I didn’t know an app could even delete entire folders from my machine and skip the trash entirely!..
Unlike the other poster, I don’t have any packages installed, as I was just learning how to use Atom and wanted to learn how to use stock first.
In case it’s of use to anyone, I’m on a Mac running macOS 10.13.3, using Atom version 1.25.1 x64. Suffice to say, I’m finding a different text editor.