`KCFGExploration.prune` and `APRProof.prune` need updated

[ehildenb]

In #601, the functionality of APRProof.prune changed. Before, it would not accidentally remove the init/target nodes, now it will allow the user to do that. Additionally, if the user uses the default behavior (without listing nodes to remove) it should automatically remove those from the nodes to consider for removal.

Before, in reachability.py:

Now:

In particular: APRProof.prune(...) should automatically add the init and target nodes to the keep_nodes list that is passed to KCFGExploration.prune(...).

This is blocking the KEVM update from pyk: runtimeverification/evm-semantics#2041