Various atmos fixes

#### Various atmos fixes

* Made manifolds instancing compatible with the maploader.

The _initialize_dir_ setting was done before the preloader could kick in.

* Fixed the runtime which happenend when a pipe was destroyed but not the meter connected to it.

The meter is now properly removed in pipe/Destroy() and fingerprints transferred.

If i missed some unfixed atmos bugs, don't hesitate to comment here.