Documentation sorely out of date

[KasperFyhn]

This project has been in the hands of many developers over time, and it shows.

The documentation is mostly on the individual components at the moment, some of which are not being used anymore, at least not in the way they are now.

The full pipeline, with run.py, configuration etc. also lacks documention. There is something under FAQ, but assuming that it should be the main entry for any user or developer, it should be one of the first things to see in a readme and the docs.