Fix for installation of desktop file

Continues  #2630
Fixes #2647
Installs desktop file with respect to `INSTALL_PREFIX`.
* `sudo script/grunt install` will install `Atom.desktop` to `/usr/local/share/applications` instead of `/usr/share/applications/`
* When a custom `INSTALL_PREFIX` is set the user will have to install the desktop file manually by copying `$INSTALL_PREFIX/share/applications/Atom.desktop` to `/usr/local/share/applications`
* Fix when `INSTALL_PREFIX` ends with `/`