You can clone with
HTTPS or Subversion.
The simulator does 'turn on' the permissions ("device-storage:pictures","storage") automatically...Is inside as developer I have to set manually everyy time that I need to delete the app and re-install.
Permissions need to be declared not for simulator, but for firefox os apps. This is for security reasons. https://developer.mozilla.org/en-US/docs/Mozilla/Firefox_OS/Security/Application_security