Revised paper

This release contains features and fixes in response to review comments in the manuscript, as well as other raised issue fixes.

New features:

• Arbitrary cluster definitions can be merged with the clusters found using --external-clustering (#30)
• A new, simpler, example has been added to the documentation
• All plots are clearer and show the unscaled distances a and pi_n (#32)

Bug fixes:

• Check distance file provided when using --assign-query (#29)
• Ensure python3 is being used (v2.7 unsupported)
• General tidying of code from pylint errors and warnings