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)

nodes/passthrough/src/passthrough_node.cpp

@@ -64,12 +64,12 @@ void PassthroughNode::process() {
     auto status = mxlFlowReaderGetGrain(*reader_, read_index_, 5000000ULL, &grain_info, &payload);
     if (status != MXL_STATUS_OK) {
         if (status == MXL_ERR_OUT_OF_RANGE_TOO_LATE || status == MXL_ERR_OUT_OF_RANGE_TOO_EARLY) {
-            auto old_index = read_index_;
             auto now = mxlGetTime();
             auto current_index = mxlTimestampToIndex(&grain_rate_, now);
             read_index_ = current_index - READ_DELAY_GRAINS;
-            spdlog::warn("Passthrough: index {} out of range ({}), realigned to {}",
-                        old_index, static_cast<int>(status), read_index_);
+            if (grains_processed_ == 0) {
+                spdlog::warn("Passthrough: realigned to index {}", read_index_);
+            }
         }
         return;
     }
@@ -94,8 +94,8 @@ void PassthroughNode::process() {
     read_index_++;
     grains_processed_++;
 
-    if (grains_processed_ <= 5 || grains_processed_ % 50 == 0) {
-        spdlog::info("Passthrough: grain #{}, index={}, size={}", grains_processed_, grain_info.index, grain_info.grainSize);
+    if (grains_processed_ == 1) {
+        spdlog::info("Passthrough: first grain processed, index={}", grain_info.index);
     }
 }