adding message passing to ensembles and inputs
fixed array compatibility
http://www.python.org/dev/peps/pep-0008/
polish the theano prototype

- add proper process termination
- remove old commented code
- safeguard against start procs multiple times in run()
- ensure setup is re-run after modifying network after a run()
Merge branch 'theano-msg'

Conflicts:
	src/distribute-proto/matrix_multiplication.py
	src/distribute-proto/nef/ensemble.py
	src/distribute-proto/nef/network.py