fix: enable atom type and master term remove functionality

[RobBuchananCompPhys]

Closes #1065, Closes #1874, Closes #1586

[trisyoungs]

Good start. However there are a couple of "propagation" mechanics to consider.

1. When removing an AtomType we are currently being saved (or perhaps being obscured from problems...) by our use of std::shared_ptr both in the main vector of AtomTypes as well as any classes which need it. A bigger discussion which arises from this is "Should we really be using something like std::weak_ptr to store references to an AtomType? For now, those references must be nullified by extending the objectNoLongerValid and removeReferenceTo template functions (see CoreData).
2. Removing a master term suffers from a similar problem to the AtomType, but when removed we should simply convert any uses into Species-local definitions (i.e. copy the data into a new SpeciesBond etc.)

Seems that there's a fair bit more work here than anticipated!