chore: phase 1 cleanup — proper shutdown, flow resource cleanup, test fix

- node_runner: track all readers/writers in flow_resources vector,
  release them via mxlReleaseFlowWriter/mxlReleaseFlowReader before
  destroying the MXL instance (fixes 'leaked flow writer' warning)
- node_runner: remove_writer/remove_reader commands now also release
  the MXL flow resources, not just reset the node's optional<>
- engine: call process_manager.stop_all(graph) on shutdown to kill
  child node processes (prevents orphaned passthrough processes)
- graph: add get_node_mut() for process_manager to update node state
- process_manager: implement stop_all(Graph&) that SIGTERMs all
  running node processes
- passthrough: reduce logging to first-grain and realign-once only
- tests: update flow format assertion to match NMOS
  (urn:x-nmos:format:video instead of video/v210)

engine/src/main.cpp

@@ -52,5 +52,6 @@ int main(int argc, char* argv[]) {
     }
 
     spdlog::info("DMF Studio Engine shutting down");
+    process_manager.stop_all(graph);
     return 0;
 }