backup task fixes

This PR should fix all of the backup related tickets.

Summary:
* rewrote some parts to get a better overview
* namespaces working
* bundels are now saved with the same path as they are stored within the repositories folder
    - no problems any more with repositories which has the same name but are stored within different namespace folders.
* empty Repositories
    - During backup:  gets discarded
    - During restore: gets recreated via Git
* Push/Pull problems after restore:
    - Hooks are now correctly linked.
    - gl-conf split error messages are now gone.