Some fixes

   * Improve npm error catching (issue #24)
   * Manage patch with empty folder (issue #25)
   * Write readable json file (config and stack) 
   * Debug update-stack function (pb reported in irc)
I know that folder autostart exists : https://github.com/poupotte/cozy-controller/blob/master/server/initialize.coffee#L110. It's the test to know if you have to apply the patch are not.