fix(serena): register new runtime markers and untrack blocker ack

The .serena/.flow_blocker_ack.json Stop-hook marker (plus
.stop_lifecycle_timeout_marker and .bootstrap_overrides.log) was missing
from the fullrepo runtime list and the knowledge-commit runtime pattern,
so a release commit captured it as tracked content and fullrepo publish
refused with a non-agent dirty error. Register all three markers in both
registries (mirroring the Claude flow plugin canon) and remove the
tracked marker file from history going forward.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: rldyourmnd

.serena/.flow_blocker_ack.json

@@ -65,6 +65,9 @@
     ".serena/.dirty_stop_ack",
     ".serena/.flow_sync_marker",
     ".serena/.flow_post_task_state.json",
+    ".serena/.flow_blocker_ack.json",
+    ".serena/.stop_lifecycle_timeout_marker",
+    ".serena/.bootstrap_overrides.log",
 )
 
 SECRET_RE = re.compile(

plugins/rldyour-flow/scripts/fullrepo_sync.py

@@ -15,7 +15,7 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 STATE_SCRIPT="$SCRIPT_DIR/serena_memory_state.py"
 
 KNOWLEDGE_PATTERN='^.. \.serena/(memories|plans|research)(/|$)'
-RUNTIME_PATTERN='^.. \.serena/(\.sync_marker|\.serena_sync_state\.json|\.auto_sync_head|\.active_workflow_intent\.json|\.dirty_stop_ack|\.flow_sync_marker|\.flow_post_task_state\.json)$'
+RUNTIME_PATTERN='^.. \.serena/(\.sync_marker|\.serena_sync_state\.json|\.auto_sync_head|\.active_workflow_intent\.json|\.dirty_stop_ack|\.flow_sync_marker|\.flow_post_task_state\.json|\.flow_blocker_ack\.json|\.stop_lifecycle_timeout_marker|\.bootstrap_overrides\.log)$'
 
 STATUS=$(git status --porcelain -uall 2>/dev/null | grep -vE "$RUNTIME_PATTERN" || true)
 if [ -z "$STATUS" ]; then