The ModelPolisher does not have any particular documentation detailing what it actually does.
This is somewhat suboptimal.

When this milestone is reached we:

Have User Manual style documentation in place that explains what the user can expect the ModelPolisher to do

The very least would be a list of specific actions that are performed (e.g. "move annotations from notes to RDF metadata", "replace RDF bqbiol:is annotations with identifiers.org IDs", "remove all bqbiol:is annotations from species that don't follow from BiGG" etc.)

Have up to date documentation in place on how to install, update and run the ModelPolisher

The Docker way of starting the application puts the bulk of the responsibility for updating in our hands.
However, Docker is not necessarily easy to set up and use for many users.
Therefore documentation (and usability) should also address these users.

Have documentation for future maintainers in place

This should at least comprise

• API docs/javadocs
• "how to" set up everything for development, in particular running a debugger
• "how to" build and test during development (w/r to the databases involved)
• where to acquire suitable testing data
• best practices for people new to git/GitHub projects
• basic "how to" use gradle

The aim should be that it is reasonably easy for maintainers who are not particularly DevOps-savy to pick up the ball.