Write docs for every module

[Jambls]

As a consumer of the project, I want every module to be documented so that I can see what things do at a glance, rather than having to dig into the code.

• Document the whole project to Javadoc standard.

Waiting on #99, #100, #101, and #102

[MHCooke]

pipe.hh should contain an overview of how pipes work and how to use them