Added fix to Cluster.py that removes the assignments, generators, and distances options and adds the output_dir option. The Assignments, etc. are therefore named in a regular manner but to the output_dir. Additionally, I removed the output for Ward's method (output_zmatrix). It behaves in the same way as the assignments. It ends up saved to output_dir.
Fixed typo in Cluster.py.
I hadn't removed the zmatrix output argument from Cluster.py yet. I just removed it now.
Cluster.py now only has the output filenames hardcoded once. I removed the check_paths function, and essentially put it in the main function. In order to get the zmatrix_fn to the cluster function, I created an empty dictionary in main (extra_kwargs) that can house any additional data necessary for the clustering step. This is then passed as kwargs to cluster. This addresses issue #127. How's this @rmcgibbo?
Merge branch 'cluster_args' of github.com:SimTk/msmbuilder into tICA