Automaton constructor does not check whether there is any path to a location

The ```Automaton``` constructor should consider checking whether all locations can be reached following the edges. If we find a location which cant be reached, then we should remove it, together with the clocks and boolean variables only present in the part of the Automaton we can remove.

Start at the Automaton constructor and inspect how locations, edges, clocks, and boolean variables are represented. Determine how unreachable locations are identified and removed, including variables used only by the removed portion; done means every retained location is reachable and no removed-only variables remain.

Written by the indexing model from the issue text.