Rewire convenience materializer APIs to staged tree flow wrappers
Refactor run_session_flow to build on the new staged tree pipeline instead of directly executing bespoke load loops. The convenience layer now derives scope/message-scope outputs from SessionTreePlan and uses run_session_tree_flow to obtain hydrated results.
Add run_session_tree_flow as a composed wrapper over plan -> resolve -> hydrate, and merge stage issues into a single surfaced report path. This keeps the old ergonomic entrypoints while making staged behavior canonical under the hood.