Atom Custom App icon
Replace the Atom application icon. Changes persist across updates and restarts.
Install
apm install custom-app-icon or search “app icon” under packages within Atom.
Setup
Simply place your custom .icns file(s)* in your ATOM_HOME directory, or specify a file path in the package settings.
* You can also supply a file.icns which will apply to all files associated with Atom.
Restore the original icon/s from the command palette.
NOTE that this package is mac only for now; you couldn't pay me enough to use Windows… but pull requests are welcome.