Bugfix. Opt logfile has to be opened for writing.
Can now specifiy tau_rc, tau_ref.

For the pre population and the cleanup population.

The parameter names are:
Cleanup: ctau_ref, ctau_rc
Pre: tau_ref, tau_rc
Removed build_cleanup_learning function.

Wasn't being used, since association_network just creates its own
cleanup ensemble.
Simplified learn.learn api and functionality.

* learn.learn no longer tries to set the cleanup intercept. Let
  association_network handle that.

* all of learn.learns parameters other than the filename now assumed to
  be packaged in the params object.
Cleaning up association_network.py
Changed what is stored in data from training
Renamed 'parameters' member to 'params'.
Fixed bug in load_simulation_data.

Now only tries to concatenate simulation data loaded from different
files if the items in question are ndarrays. Otherwise just takes the
item that was loaded earlier.
Tidying up dodo.py.

* Using mytools.make_filename for all filenames.

* Changed tasks to comply with new function signature for learn.learn.

* Fixed it so that all parameters are set in the call to
  Parameters.__init__. Makes it so that all parameters are set in one
  place, much tidier.

* The only parameters not included in Parameters.__init__ are those
  relevant for determining the tests that are run, as you can make a
  case that these are conceptually distinct. i.e. we build a model and
  have it learn, and then the question of what tests you run on that
  model is completely separate.
Added more parameters to optimization process.
Tidying up optimize.py.