documentation + small fixes

Hi, 
please review my changes and pick what you like. I'm preparing more clean-up stuff, parallel works, some RNN and crossvalidation, but I'd like this merged first so we have same baseline. 

It's mostly documentation, some marked TODOs so we know what needs to explain, small fixes, descriptions to plots. 

Notable changes: 
bring common functionality to network structure (eg. nn.momentum). 
plot,numepochs,batchsize is there, renamed learning_Rate to alpha (as used in most other classes of the toolbox), dropout is a percentage now. 

Have a nice spring! :)