New API ensemble to ensemble connections progress

- Not quite working, but doesn't raise an exception
- Also some work on 2drep and controlledintegrator IPython notebook
- Made a separate file for probes (similar to connections.py)
Changes to connections

- Filter now respected on SimpleConnection
- DecodedConnection logic improved
- Updated new API controlledintegrator example
- New API controlledintegrator is now closer to the right answer,
  but not quite there yet
controlledintegrator works in new API

- There were a few dt issues
- Seems to work, though not with tau=0.1 (too strong?)
  - Kind of fragile though