Fix run and submit_topology commands.

Print stack traces when we run and things break and don't try to be smart about the .clj topology definition file, just accept it as a positional argument.
Now that we have streamparse on clojars, drop the clj and main from bootstrap project.clj files. #7
Specify time to run local topology in seconds, not milliseconds.
PEP8 fixes (indentation).
Begin work on sparse deploy command (WIP). #1