Run swarm cli

### Extracted CLI from Permutations Runner. …

- Pulled all options parsing into run_swarm.py.
- Refactored runPermutations into lots of little pieces.
- Replaced runPermutations with three functions:
  - runWithConfig (accepts config dict)
  - runWithJsonFile (accepts path to JSON config file)
  - runWithPermutationsScript (accepts path to permutations.py)
- Updated run_swarms to call into permutations_runner.runWithJsonFile or
  .runWithPermutationsScript

So CLI is still intact, and new public functions exist for using the `permutations_runner` directly:

- nupic.swarming.permutations_runner.runWithConfig
- nupic.swarming.permutations_runner.runWithJsonFile
- nupic.swarming.permutations_runner.runWithPermutationsScript

Fixes #762.