Make process.exit() quit gracefully

Instead of abrupting the whole program immediately, we should close all
windows and release all native resources gracefully on exit. This avoids
possible crashes.

Fix #3350.

atom/browser/api/lib/app.coffee

@@ -50,7 +50,6 @@ app.getAppPath = ->
 # Be compatible with old API.
 app.once 'ready', -> @emit 'finish-launching'
 app.terminate = app.quit
-app.exit = process.exit
 app.getHomeDir = -> @getPath 'home'
 app.getDataPath = -> @getPath 'userData'
 app.setDataPath = (path) -> @setPath 'userData', path