Enhance cufflinks for Dataset Collections

![Enable workflows over many replicates](http://i.imgur.com/Ce8zcsG.png)

 - Use multi-data input in several spots instead of repeats. (Currently downside of multiple inputs versus repeats is that they don't allow duplicate inputs via UI (API allows it) - is there ever any reason for these inputs to pass same file twice?).
 - Updated cuffdiff/cuffnorm for even more sophisticated potential collection use cases if conditions are identifiers to 1-D `list` of samples or 2-D list (`list:list`) with many samples per condition.