fix(serena): persist semantic sync acknowledgements

Author: rldyourmnd

plugins/rldyour-serena-mcp/scripts/commit_serena_knowledge.sh

@@ -11,13 +11,29 @@ fi
 ROOT=$(git rev-parse --show-toplevel 2>/dev/null || pwd)
 cd "$ROOT"
 HEAD_FULL=$(git rev-parse HEAD 2>/dev/null || true)
+GIT_COMMON_DIR=$(git rev-parse --git-common-dir 2>/dev/null || true)
+if [ -n "$GIT_COMMON_DIR" ] && [[ "$GIT_COMMON_DIR" != /* ]]; then
+  GIT_COMMON_DIR="$ROOT/$GIT_COMMON_DIR"
+fi
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 STATE_SCRIPT="$SCRIPT_DIR/serena_memory_state.py"
 
 KNOWLEDGE_PATTERN='^.. \.serena/(memories|plans|research)(/|$)'
 RUNTIME_PATTERN='^.. \.serena/(\.sync_marker|\.serena_sync_state\.json|\.auto_sync_head|\.active_workflow_intent\.json|\.dirty_stop_ack|\.flow_sync_marker|\.flow_post_task_state\.json|\.flow_blocker_ack\.json|\.stop_lifecycle_timeout_marker|\.bootstrap_overrides\.log)$'
 
+write_sync_ack() {
+  if [ -z "$HEAD_FULL" ]; then
+    return 0
+  fi
+  mkdir -p .serena
+  printf "%s\n" "$HEAD_FULL" > .serena/.auto_sync_head
+  if [ -n "$GIT_COMMON_DIR" ]; then
+    mkdir -p "$GIT_COMMON_DIR/rldyour"
+    printf "%s\n" "$HEAD_FULL" > "$GIT_COMMON_DIR/rldyour/serena_auto_sync_head"
+  fi
+}
+
 STATUS=$(git status --porcelain -uall 2>/dev/null | grep -vE "$RUNTIME_PATTERN" || true)
 if [ -z "$STATUS" ]; then
   if [ ! -f "$STATE_SCRIPT" ]; then
@@ -32,10 +48,7 @@ if [ -z "$STATUS" ]; then
   MEMORY_CURRENT=$(printf "%s" "$STATE_JSON" | python3 -c 'import json,sys; data=json.load(sys.stdin); print("true" if (data.get("memory_matches_head") or data.get("memory_semantically_current")) else "false")' 2>/dev/null || echo "false")
   if [ "$MEMORY_CURRENT" = "true" ]; then
     rm -f .serena/.sync_marker .serena/.serena_sync_state.json
-    if [ -n "$HEAD_FULL" ]; then
-      mkdir -p .serena
-      printf "%s\n" "$HEAD_FULL" > .serena/.auto_sync_head
-    fi
+    write_sync_ack
     echo "Serena knowledge is current; removed runtime sync markers"
     exit 0
   fi
@@ -86,10 +99,7 @@ if [ -z "$TRACKED_KNOWLEDGE" ]; then
     exit 1
   fi
   rm -f .serena/.sync_marker .serena/.serena_sync_state.json
-  if [ -n "$HEAD_FULL" ]; then
-    mkdir -p .serena
-    printf "%s\n" "$HEAD_FULL" > .serena/.auto_sync_head
-  fi
+  write_sync_ack
   echo "Serena knowledge is fullrepo-managed; removed runtime sync markers without committing to the current branch"
   exit 0
 fi
@@ -103,6 +113,4 @@ fi
 git commit -m "chore(serena): sync project knowledge after ${HEAD_SHORT}"
 HEAD_FULL=$(git rev-parse HEAD 2>/dev/null || true)
 rm -f .serena/.sync_marker .serena/.serena_sync_state.json
-if [ -n "$HEAD_FULL" ]; then
-  printf "%s\n" "$HEAD_FULL" > .serena/.auto_sync_head
-fi
+write_sync_ack

plugins/rldyour-serena-mcp/scripts/serena_memory_state.py

@@ -12,6 +12,7 @@
 MEMORY_DIR = Path(".serena/memories")
 SYNC_STATE = Path(".serena/.serena_sync_state.json")
 AUTO_SYNC_HEAD = Path(".serena/.auto_sync_head")
+GIT_LOCAL_AUTO_SYNC_HEAD = Path("rldyour/serena_auto_sync_head")
 ANALYZE_SCRIPT = Path(__file__).resolve().parent / "analyze_sync_scope.py"
 SERENA_KNOWLEDGE_PREFIXES = (
     ".serena/memories/",
@@ -42,6 +43,17 @@ def _stdout(*args: str) -> str:
     return _git(*args).stdout.strip()
 
 
+def _git_common_dir() -> Path | None:
+    proc = _git("rev-parse", "--git-common-dir")
+    if proc.returncode != 0:
+        return None
+    value = proc.stdout.strip()
+    if not value:
+        return None
+    path = Path(value)
+    return path if path.is_absolute() else Path.cwd() / path
+
+
 def _resolve_commit(ref: str) -> tuple[str, str] | None:
     proc = _git("rev-parse", f"{ref}^{{commit}}")
     if proc.returncode != 0:
@@ -169,13 +181,20 @@ def _load_sync_state() -> dict[str, Any]:
 
 
 def _acknowledged_head_matches(head_full: str, head_short: str) -> bool:
-    if not AUTO_SYNC_HEAD.is_file():
-        return False
-    try:
-        value = AUTO_SYNC_HEAD.read_text(encoding="utf-8").strip()
-    except OSError:
-        return False
-    return bool(value) and value in {head_full, head_short}
+    candidates = [AUTO_SYNC_HEAD]
+    git_common_dir = _git_common_dir()
+    if git_common_dir is not None:
+        candidates.append(git_common_dir / GIT_LOCAL_AUTO_SYNC_HEAD)
+    for path in candidates:
+        if not path.is_file():
+            continue
+        try:
+            value = path.read_text(encoding="utf-8").strip()
+        except OSError:
+            continue
+        if value and value in {head_full, head_short}:
+            return True
+    return False
 
 
 def _memory_candidates(head_short: str) -> tuple[int, bool, list[tuple[str, str]]]:

scripts/smoke_serena_memory_taxonomy.sh

@@ -276,8 +276,13 @@ test "$BEFORE" = "$AFTER" || fail "commit_serena_knowledge created a commit in f
 test ! -e .serena/.sync_marker || fail "sync marker was not cleared"
 test ! -e .serena/.serena_sync_state.json || fail "sync state was not cleared"
 test -e .serena/.auto_sync_head || fail "auto sync acknowledgement was not written"
+GIT_COMMON_DIR=$(git rev-parse --git-common-dir)
+test -e "$GIT_COMMON_DIR/rldyour/serena_auto_sync_head" || fail "git-local auto sync acknowledgement was not written"
 ACK_CURRENT=$(python3 "$STATE_SCRIPT" | python3 -c 'import json,sys; print("true" if json.load(sys.stdin).get("is_current") else "false")')
 test "$ACK_CURRENT" = "true" || fail "semantic ancestor acknowledgement did not leave Serena state current"
+rm -f .serena/.auto_sync_head
+ACKLESS_CURRENT=$(python3 "$STATE_SCRIPT" | python3 -c 'import json,sys; print("true" if json.load(sys.stdin).get("is_current") else "false")')
+test "$ACKLESS_CURRENT" = "true" || fail "semantic ancestor state depended on worktree runtime acknowledgement marker"
 
 STALE_REPO="$TMP_ROOT/stale"
 mkdir "$STALE_REPO"