<p dir="auto">This happened after I switched branches in git, and had folder open, which was unavailable in branch that I switched to.<br>
Atom was open in background, GitHub app was on top.</p>
<p dir="auto">Right-click in the tree view to rename a file (which is currently open in the editor) and the file gets copied/duplicated to the new name while the old file remains open. They are not symlinked as editing one does not produce changes in the other after closing/reopening.</p>
<p dir="auto">Renaming a directory (containing a file open in the editor) has similar effect. The old directory remains, including any files currently open in the editor. Everything else is moved to the new directory, including copies of open files.</p>
<p dir="auto">Atom 0.170 on OS X 10.10. Has been happening for a while, and happens even when all plugins are disabled. I tested by opening my Desktop folder in Atom, creating a folder and some files, and renaming the folder while with some files open.</p>