Comment all the things

[recursion-ninja]

We rushed a bunch of stuff into product. Need to comment this code for maintainability.

Requires more documentation:

• [x] Nexus parser
• [x] PhylogeneticDAG types
• [x] Resolution aware post-order traversal
• [x] Resolution aware pre-order traversal
• [x] Ukonnen matrix math

[recursion-ninja]

We should add a checkbox list of places where documentation needs to be added/improved.

[recursion-ninja]

Adding documentation to the Nexus parser is all that's left.

[recursion-ninja]

We have documented all exported functions. We just need to keep the documentation coverage at 100%