Discuss package structure and improve API reference

[ielis]

We need to discuss the API of the library. Things like:

• pros and cons of keeping all data/value definitions in a single package (e.g. genophenocorr.model)
• creating a package with code for taking input data, such as phenopackets, Phenopacket Schema Cohort, and turn it into the internal representation. This includes the code for variant/protein annotation, basically everything we need to do before we get genophenocorr.Cohort. My suggestion is to put the code into genophenocorr.preprocess.

When we're happy with the package structure, we can setup the __init__.py files to play with make doctest and enable generation of the API reference documentation sections.