tree: automatically remove intermediate files with option to disable clean up

[joverlee521]

Originally discussed in Slack with @huddlej

Currently, augur tree automatically removes intermediate tree builder files within each tree building function. The tree building functions all default to clean_up=True, but do not expose this as a CLI option so users cannot disable the clean up. On the other hand, the Augur specific intermediate files, masked_alignment_file and informative_sites, are never cleaned up. These can be confused as "outputs" of the command that are then mistakenly used for downstream analysis.

Ideally, all intermediate files are cleaned up by default and there's a CLI option to disable the clean up (e.g. --no-clean-up) for debugging purposes.

[tsibley]

I'd add that besides a CLI option, this is the sort of thing where an environment variable is super handy.