Deal with runFlow/run blocker on 0.9.0

This is probably better, but the whole Job, CascadeJob, Tool, etc... family have been neglected from the design for too long.

We need to address this in 0.10. There are several issues:

1) What exactly is a "Job"?
2) What is the responsibility of Tool, and what of Job?
3) How can I get out of this framework of Job, and just run as a Library? (possible now, but so unclear to people, only summingbird has done it).