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/include/dmf-engine/graph.hpp

@@ -42,6 +42,7 @@ public:
     NodeId add_node(const std::string& type, const nlohmann::json& config = {});
     bool remove_node(const NodeId& node_id);
     const GraphNode* get_node(const NodeId& node_id) const;
+    GraphNode* get_node_mut(const NodeId& node_id);
     std::vector<GraphNode> get_nodes() const;
 
     EdgeId add_edge(const NodeId& from_node, const PortId& from_port,

libs/dmf-engine/include/dmf-engine/process_manager.hpp

@@ -12,6 +12,7 @@ public:
     bool start_node(GraphNode& node, const std::string& mxl_domain, uint16_t base_port);
     bool stop_node(GraphNode& node);
     void stop_all();
+    void stop_all(Graph& graph);
 
     bool is_running(const NodeId& node_id) const;