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.

* Freezers, heaters and cryo cells now properly initialize on construction.

Had to add a _/obj/machinery construction() proc_ that is called on machinery construction (i.e screwing a completed machine frame), but not on machinery _New()_.

This fixes  #5118 and, 21 and 22 of #6351.

* Made engineers less clumsy : wrench rotating is always clockwise 90° instead of a random dir now.

If i missed some unfixed atmos bugs, don't hesitate to comment here.