Rearchitect BaseModel and subclasses to permit extensive sharing of SiteModels and SubstitutionModels

[lmaurits]

This is basically the reincarnation of #160, which became less ambitious for the sake of 1.4.0 when it was realised that doing this properly requires quite a bit of thought and testing.

Basically, we should strive to always use as few instances of TreeLikelihood, SiteModel and SubstitutionModel as possible by sharing what we can. This interacts in non-trivial ways with at least the following (and possibly more):

• Rate variation
• Feature state space size
• Equillibrium frequency settings
• Ancestral State Reconstruction
• Pruned Trees