fix(codex): resolve peer-review findings R1-R6 and T1-T2

- R1: use herdr send-keys C-c for graceful stop
- R2: preserve JSONL fallback discovery when database is empty
- R3: apply workspace-scoped SQLite query before bounding results
- R4: tighten artifact validation to fail closed on missing/invalid metadata
- R5: verify actual rollout presence before reporting resumable in status
- R6: remove unconditional drift-B backend command fallback
- T1: parameterize artifact metadata regression with verified finder fixture
- T2: seed unmanaged and managed sessions in mock herdr for drift-B testing
- Add final loop review reports (100% PASS)

.agents/skills/lib_py/agents/adapters/codex.py

@@ -73,17 +73,33 @@ class CodexAgentAdapter(BaseAgentAdapter):
             return False
         if ctx.epoch and os.path.getmtime(path) < ctx.epoch:
             return False
-        found_cwd = db_cwd
-        if not found_cwd:
-            try:
-                with open(path) as f:
-                    first = f.readline()
-                found_cwd = json.loads(first).get('payload', {}).get('cwd')
-            except Exception:
+
+        # Fail closed on invalid metadata or mismatched id / cwd (R4)
+        try:
+            with open(path) as f:
+                first = f.readline().strip()
+            meta = json.loads(first)
+            if not isinstance(meta, dict):
                 return False
-        if found_cwd and workspace_key(found_cwd) != workspace_key(ctx.cwd):
+            payload = meta.get('payload')
+            if not isinstance(payload, dict):
+                return False
+            file_id = payload.get('id')
+            file_cwd = payload.get('cwd')
+            if not file_id or file_id != uuid:
+                return False
+            if not file_cwd:
+                return False
+            if db_cwd and workspace_key(db_cwd) != workspace_key(file_cwd):
+                return False
+            target_cwd = ctx.cwd or ctx.workspace
+            if not target_cwd:
+                return False
+            if workspace_key(file_cwd) != workspace_key(target_cwd):
+                return False
+            return True
+        except Exception:
             return False
-        return True
 
     def purge_artifacts(self, uuid: str, ctx: DiscoveryContext) -> List[str]:
         purged = []
@@ -126,7 +142,13 @@ class CodexAgentAdapter(BaseAgentAdapter):
         return os.path.exists(f"{codex_home}/auth.json") or bool(os.environ.get('OPENAI_API_KEY'))
 
     def discover(self, ctx: DiscoveryContext) -> List[str]:
+        target_ws = ctx.workspace or ctx.cwd
+        target_key = workspace_key(target_ws) if target_ws else ""
+
         db = self._state_db(ctx)
+        candidates = []
+        seen = set()
+
         if db and os.path.exists(db):
             try:
                 conn = sqlite3.connect(db)
@@ -135,24 +157,53 @@ class CodexAgentAdapter(BaseAgentAdapter):
                 cols = {r[1] for r in cur.fetchall()}
                 order_col = "updated_at" if "updated_at" in cols else ("created_at" if "created_at" in cols else None)
                 order_clause = f"ORDER BY {order_col} DESC" if order_col else ""
-                rows = conn.execute(
-                    f"SELECT id, cwd FROM threads {order_clause} LIMIT 50"
-                ).fetchall()
+
+                # Query database with workspace scope before bounding (R3)
+                if "cwd" in cols and target_ws:
+                    direct_cwds = list({target_ws, os.path.realpath(target_ws)})
+                    placeholders = ",".join("?" * len(direct_cwds))
+                    cur.execute(f"SELECT id, cwd FROM threads WHERE cwd IN ({placeholders}) {order_clause} LIMIT 50", direct_cwds)
+                    for uuid, cwd in cur.fetchall():
+                        if uuid and uuid not in seen and self.verify_artifact(uuid, ctx):
+                            candidates.append(uuid)
+                            seen.add(uuid)
+
+                # Page through batches if needed to catch symlink aliases / canonical paths
+                if len(candidates) < 50:
+                    cur.execute(f"SELECT id, cwd FROM threads {order_clause}")
+                    while True:
+                        batch = cur.fetchmany(100)
+                        if not batch:
+                            break
+                        for uuid, cwd in batch:
+                            if uuid in seen:
+                                continue
+                            if target_key and cwd and workspace_key(cwd) != target_key:
+                                continue
+                            if uuid and self.verify_artifact(uuid, ctx):
+                                candidates.append(uuid)
+                                seen.add(uuid)
+                                if len(candidates) >= 50:
+                                    break
+                        if len(candidates) >= 50:
+                            break
                 conn.close()
-                candidates = []
-                for uuid, cwd in rows:
-                    if ctx.workspace and cwd and workspace_key(cwd) != workspace_key(ctx.workspace):
-                        continue
-                    if uuid and self.verify_artifact(uuid, ctx):
-                        candidates.append(uuid)
-                return candidates
             except Exception:
                 pass
+
+        # R2: If database yielded usable candidates, return them; otherwise fall through to transcript discovery
+        if candidates:
+            return candidates
+
         root = self._codex_home(ctx)
-        candidates = []
-        paths = sorted(glob.glob(f"{root}/sessions/*/*/*/rollout-*.jsonl"), key=os.path.getmtime, reverse=True)[:50]
+        paths = sorted(glob.glob(f"{root}/sessions/*/*/*/rollout-*.jsonl"), key=os.path.getmtime, reverse=True)
         for path in paths:
-            uuid = os.path.basename(path)[:-6][-36:]
-            if uuid and self.verify_artifact(uuid, ctx):
-                candidates.append(uuid)
+            base = os.path.basename(path)
+            if base.endswith(".jsonl") and len(base) >= 42:
+                uuid = base[:-6][-36:]
+                if uuid and uuid not in seen and self.verify_artifact(uuid, ctx):
+                    candidates.append(uuid)
+                    seen.add(uuid)
+                    if len(candidates) >= 50:
+                        break
         return candidates

.agents/skills/multi-agent-mux-monitor/scripts/reconcile.sh

@@ -547,10 +547,6 @@ if herdr_confirmed:
                 except Exception:
                     pass
 
-        if not agent:
-            if pm_check and pm_check.get('cmd') in ('claude', 'agy', 'hermes', 'grok', 'opencode', 'codex'):
-                agent = pm_check['cmd']
-
         if not agent:
             continue
 

.agents/skills/multi-agent-mux-status/scripts/status.sh

@@ -139,8 +139,6 @@ def resume_on_disk(s):
                     conn.close()
                     if r and r[0] and os.path.exists(r[0]):
                         return 'yes'
-                    if r:
-                        return 'yes'
                 except Exception:
                     pass
             m = glob.glob(f"{codex_home}/sessions/*/*/*/rollout-*-{u}.jsonl")
@@ -340,8 +338,6 @@ def resume_on_disk(s):
                     conn.close()
                     if r and r[0] and os.path.exists(r[0]):
                         return 'yes'
-                    if r:
-                        return 'yes'
                 except Exception:
                     pass
             m = glob.glob(f"{codex_home}/sessions/*/*/*/rollout-*-{u}.jsonl")

.agents/skills/multi-agent-mux-stop/scripts/stop_session.sh

@@ -198,7 +198,11 @@ graceful_stop() {
   pane_pid=$(herdr list-panes -t "$SESSION_NAME" -F '#{pane_pid}' 2>/dev/null | head -1 || true)
   exitkey="$("$(_delegate_py_bin)" -m lib_py.agents exit-key "$AGENT" 2>/dev/null || echo "/exit")"
   echo "graceful: send-keys '$exitkey' to $SESSION_NAME"
-  send_keys_safe "$SESSION_NAME" "$exitkey" "stop$$" || echo "graceful: safe delivery failed (rc=$?) — falling back to kill chain"
+  if [ "$exitkey" = "Ctrl+C" ] || [ "$exitkey" = "C-c" ]; then
+    herdr send-keys -t "$SESSION_NAME" C-c 2>/dev/null || true
+  else
+    send_keys_safe "$SESSION_NAME" "$exitkey" "stop$$" || echo "graceful: safe delivery failed (rc=$?) — falling back to kill chain"
+  fi
   _wait_session_gone "$SESSION_NAME" 5 || true
   if ! herdr has-session -t "$SESSION_NAME" 2>/dev/null; then
     echo "graceful: exited cleanly"