Clean up folders and output chatter

[snacktavish]

• Many of the folders on the main page of the repo can be organized into a sub-dir
• Evaluate the level of chatter in a standard run, and the spelling. Make some cuts if poss
• Clean up the outputs folder so that best_ref.* and the other random files go somewhere organized.
• maybe change the internal outputs to 'results'
• maybe change combine_and_infer to something more intuitive?

[snacktavish]

Specially "random alignment" statements are sort of mysterious

[jtfield]

3 tasks down. the last 3 will take a little more time.