Started a new branch to add regularization and momemntum to the SdA code.  Now to compile and test it tonight.
Ready to test implementation of momentum, weight decay in SdA models.

L.
Added a boolean switch to make the logistic regression layer optional.
Added a switch in the generation of updates for SdA pretraining functions so that un-tracked parameters don't get updated.  I'm not sure if this is quite the right thing to do: the biases of the dAs will not be updated with momentum, but the model parameters shared with the MLP will.
Added debugging statements to the pretraining function code in SdA, where I've encountered a strange type error.  Also corrected the documentation in hidden layer, and made the test script use a GPU.
Removed explicit assignment of theano to gpu, see if I still encounter the TypeError bug.
Interesting: named parameters in functions correspont to the 'name' string in the declarations of T.<variable_type>.  This should get rid of the 'momentum' not being found error.
Removed the debugging statements in SdA for type changes, and changed the specs of the test model for weight decay and momentum.