Refactor CompartmentType, etc

[ArtPoon]

Our terminology is confusing. I propose the following changes:
CompartmentType -> Compartment
Compartment -> Deme

[ArtPoon]

Revisiting this, I think it is still appropriate to rename CompartmentType to Compartment, but what we currently call Compartment is a single host that has been sampled. We might have to rename Compartment to SampledHost to make this explicit.

[ArtPoon]

Renaming as follows:

Old name	New name	Definition
CompartmentType	Deme	A well-mixed subpopulation of host individuals sharing the same attributes
Compartment	Host	A host individual from whom we have sampled one or more Pathogen lineages. Must belong to a Deme (inherits attributes from the Deme class). Related to other host individuals via branches of the "outer" tree.
Lineage	Pathogen	A pathogen lineage within a host individual. Comprises the branches of the "inner" tree.

[ArtPoon]

Deme (prev. CompartmentType) attributes / event types:

Old name	New name	Definition
Transition	Migration	Movement of a host individual from one Deme to another Deme (acquiring the attributes of that Deme)
Branching	Transmission	An infected host transmits their infection to an uninfected host
Migration	Superinfection	An infected host transmits their infection to another infected host

[ArtPoon]

Created new branch renaming

[ArtPoon]

I am completely revamping how we simulate population dynamics and outer trees.
Closing, and opening new issue