Address alpha issues

[gwm17]

A bunch of small changes aimed at addressing issues #27 #18 #19 #20 #21 and #24.

Highlights:

• Scale factor in clustering min size with small cutoff.
• Non-production solvers were removed, separated to independent branches.
• Fix some formatting.
• Fix particle_id.ipynb. Requires addition of matplotlib and ipympl for this notebook specifically.

Added dependencies: matplotlib, ipympl

Documentation was updated.