Protocol writing

[mhturner]

The current way of writing protocols could be simplified

[mhturner]

A change to the data / params saving structure to keep in mind for updating protocol code:
-The series_xxx level of data file now saves out protocol params (user entered in GUI), so no need to save that out in individual epochs anymore.
-Epoch and convenience params get saved at the same level in each epoch, so any attributes with the same name will be overwritten. Make sure your convenience params don't share names with epoch params