atom, atom-beta: Fixing Exec= line in app launcher

Prior to this commit the application launchers of Atom and Atom Beta executed `/usr/bin/${pname}` instead of what it is meant to `$out/bin/${pname}`. This is because upstream changed the `Exec=` line from `Exec=/usr/share/${pname}/${pname}` to `Exec=/usr/bin/${pname}` and the `substituteInPlace` line that was in the default.nix file was not appropriately adjusted.