[RAP-318] Additional cleanup of leftover files by e.g. Toil

Addresses a few leftover files that Toil leaves behind even on successful runs as outlined in RAP-318. Changes include:

• --bypass-file-store is only used in combination with Slurm.
• --stats removed since that interferes with Toil cleaning up temporary files (I don't think output of this is used?).
• ToilRunner's teardown method now parses Toil's worker logs to clean up their temporary directories unless the run is in debug mode.