Automaton constructor Clocks and Boolean variables

The ```Automaton``` constructor takes a list of ```Clock``` and one with ```BoolVar```. We should consider checking whether all clocks and boolean variables are present in the guards and update.

Start at the Automaton constructor and inspect how its Clock and BoolVar lists relate to guards and updates. Clarify the intended validation for variables absent from those expressions, then add coverage for constructor cases involving missing clocks or boolean variables; done means the constructor consistently enforces the decided rule.

Written by the indexing model from the issue text.