Review repo / code organization; write development guide.

[jonn-smith]

This repo is getting pretty big. We should review how it's being organized and write a development guide so we can formalize both our choices and how we prefer to do things.

In particular, we may want to break out some of the meatier docker images into their own repo.

This warrants several discussions.

[bshifaw]

The development guide part of this ticket might be done See the following site: https://broadinstitute.github.io/long-read-pipelines/development_guide/