added function to clean out folders

A couple of users had reported issues with analyses tanking when they
try and use half-baked results. Mostly it's just that users were
freaked out by the warning messages. Keeping these files around results
in such marginal speedups that it seems more prudent and safer to just
routinely delete them between analyses.

The default is now to clean out the phylofiles folder when the analyses
starts. This can be overriden using the --save-phylofiles commandline
option.