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)

libs/dmf-engine/src/graph.cpp

@@ -51,6 +51,11 @@ const GraphNode* Graph::get_node(const NodeId& node_id) const {
     return it != nodes_.end() ? &it->second : nullptr;
 }
 
+GraphNode* Graph::get_node_mut(const NodeId& node_id) {
+    auto it = nodes_.find(node_id);
+    return it != nodes_.end() ? &it->second : nullptr;
+}
+
 std::vector<GraphNode> Graph::get_nodes() const {
     std::vector<GraphNode> result;
     for (const auto& [_, node] : nodes_) {