More work on the manual

NB. It doesn't gel with the actual program, yet. One thing at a time.
Also, I will need to update this again before the final release, to
reflect whatever we do with the default settings for the new algorithm.
quicker config checking in config.py

I was running a check on all the subset files. Unnecessary. Can just do
it the EAFP way...
fixed a bug in the greediest algorithm

that only showed up when the best scheme was the start scheme.