algo: redesign NPDTA run

I redesigned the algorithm to make it similar to NPDA run implementation, most
importantly to handle cycles, also not even the very basic test that I
introduced didn't pass.

Additionaly, the graphStructuredStacks used to track the pushdown store and output were
incorrectly parametrized with InputSymbolType instead of PushdownStoreSymbolType
and OutputSymbolType.