Removed out-of-date comment from old_api
Cleanup test dir

Running nosetests in the project should now
* complete successfully
* pass >= three tests
* skip the rest of them.
Reorganization of nonlinear.py

Moved Sim* classes to simulator.py, but kept math in nonlinear.py
Upgrade old_api.py to use refactored sim objects

Mainly this is work in the Ensemble-creation logic.
Implement old_api make_input using Direct mode
Simulator workaround annoying np.dot semantics
Revert crippling of test_old_api
Relax test_old_api with new make_input

New make_input using Direct mode makes decoded signal show up a timestep later
than before.  This is tested directly in test_simulator, so I removed
the assert from test_old_api.
Relaxed tolerance on test_api fast probe

Recent refactoring means that the old seed is interpreted differently,
resulting in a slightly less-accurate fast probe. The other probes are
as accurate as before.