Enable using proof heirarchy from depends clauses

[ehildenb]

Blocked on: runtimeverification/pyk#663
Blocked on: #2098
Blocked on: #2092

This takes the output of APRProof.from_spec_modules and discharges them in order. In particular:

• Take advantage of the existing topological sort of APRProof.from_spec_modules
• Do not discharge super proofs until the subproofs are discharged.
• Removes two now unused helpers: claim_dependency_graph and ensure_k_sequence_on_k_cell.

[ehildenb]

Closing due to age.