Meta: Refactoring for version 0.3

[andrey-kuprianov]

This is a meta-issue to keep track of refactorings necessary for the version 0.3, to be release end of August.
We will not do a complete refactoring to fully implement #2; instead we will do a sequence of simple steps, each making the tool more reliable and easier to use.

The tasks are listed in the approximate order of their execution, but some can be done in parallel.

• Refactor error handling #53
• Reliable extraction of counterexample traces #58
• Reintroduce generic artifacts #61
• Rework Apalache module #62
• Rework TLC module #63
• Allow to select model checker version #54 (postponed to v.0.4)
• Extend integration tests #64 (postponed to v.0.4)

[andrey-kuprianov]

Closing as all tasks are either done or postponed to the next version