Meeko CLI Revision

[psharma-sr]

Revise the CLI so that it has more options and support for logging.

In particular we want to focus on making all of the information on what has happened during template matching available for logging, and then make those logging options configurable in some way for people calling Meeko.

The example given had to do with the ambiguous templates, we want to create some sort of data structure that will handle all of the tracking for these template matching scenarios (ex: if the template couldn't be matched because of too few or too many hydrogens)

Also: make sure the CLI is well-designed and accessible, add testing for CLI operations, and potentially move some of the functions out of the mk-prepare scripts into places where they are better organized and easier to access.