fix(agent): apply persist override to the DB row only, never the live list (#48677)

The persist user-message override was applied in place to the live messages
list. On the early crash-resilience persist (which runs BEFORE api_messages is
built), that stripped observed group-chat context off the live user message and
silently dropped it when observe_unmentioned_group_messages was enabled.

Fix at the single chokepoint: _flush_messages_to_session_db resolves the
override (idx/content/timestamp) locally and applies it ONLY to the row written
to the DB — the live dict is never mutated, so EVERY persist caller (early
persist, mid tool-loop flush, /resume, /branch) is protected uniformly. This
supersedes the earlier shallow-copy approach, which broke the intrinsic
_DB_PERSISTED_MARKER idempotency (copies never propagated the marker back to
the live dicts → duplicate rows) and closes the sibling class tracked in #56303.

Trailing empty-response scaffolding is still dropped from the live list in
_persist_session (unchanged behavior).

Salvaged from #48817; chokepoint reworked to coexist with the marker-based
dedup (#50372).

Co-authored-by: kyssta-exe <kyssta-exe@users.noreply.github.com>

run_agent.py

@@ -1649,9 +1649,17 @@ class AIAgent:
         """Save session state to both JSON log and SQLite on any exit path.
 
         Ensures conversations are never lost, even on errors or early returns.
+
+        Trailing empty-response scaffolding is dropped from the live list in
+        place (it is ephemeral junk the real transcript should shed). The
+        persist user-message *override* is NOT applied here — it is resolved
+        inside ``_flush_messages_to_session_db`` and written only to the DB row,
+        never mutating the live message list used by the API call (#48677 is
+        thus closed for every persist caller, not just this one).
         """
+        # Scaffolding removal mutates the live list (desired — ephemeral
+        # retry/failure sentinels must not survive into the real transcript).
         self._drop_trailing_empty_response_scaffolding(messages)
-        self._apply_persist_user_message_override(messages)
         self._session_messages = messages
         self._save_session_log(messages)
         self._flush_messages_to_session_db(messages, conversation_history)
@@ -1742,7 +1750,18 @@ class AIAgent:
             return
         if not self._session_db:
             return
-        self._apply_persist_user_message_override(messages)
+        # Persist user-message override (#48677 chokepoint): historically this
+        # mutated the live `messages` list in place, which — on the early
+        # crash-resilience persist that runs BEFORE the API call is built —
+        # stripped observed group-chat context off the live user message and
+        # silently dropped it. Instead, resolve the override here and apply it
+        # ONLY to the value written to the DB (see the write loop below); the
+        # live dict is never mutated, so every caller (early persist, mid-loop
+        # flush, /resume, /branch) is protected uniformly. Timestamp override is
+        # metadata and is likewise applied only to the written row.
+        _ov_idx = getattr(self, "_persist_user_message_idx", None)
+        _ov_content = getattr(self, "_persist_user_message_override", None)
+        _ov_timestamp = getattr(self, "_persist_user_message_timestamp", None)
         try:
             # Retry row creation if the earlier attempt failed transiently.
             if not self._session_db_created:
@@ -1784,7 +1803,7 @@ class AIAgent:
                 if isinstance(item, dict)
             }
 
-            for msg in messages:
+            for _msg_idx, msg in enumerate(messages):
                 if not isinstance(msg, dict):
                     continue
                 # Never write ephemeral recovery scaffolding to the session
@@ -1808,6 +1827,16 @@ class AIAgent:
                     continue
                 role = msg.get("role", "unknown")
                 content = msg.get("content")
+                _row_timestamp = msg.get("timestamp")
+                # Apply the persist override to THIS row's written values only
+                # (never to the live dict). Match the original guard: text-only
+                # content is replaced; multimodal (list) content is left intact
+                # so image/audio blocks aren't clobbered by the text override.
+                if _ov_idx == _msg_idx and msg.get("role") == "user":
+                    if _ov_content is not None and not isinstance(content, list):
+                        content = _ov_content
+                    if _ov_timestamp is not None:
+                        _row_timestamp = _ov_timestamp
                 # Persist multimodal tool results as their text summary only —
                 # base64 images would bloat the session DB and aren't useful
                 # for cross-session replay.
@@ -1843,7 +1872,7 @@ class AIAgent:
                     reasoning_details=msg.get("reasoning_details") if role == "assistant" else None,
                     codex_reasoning_items=msg.get("codex_reasoning_items") if role == "assistant" else None,
                     codex_message_items=msg.get("codex_message_items") if role == "assistant" else None,
-                    timestamp=msg.get("timestamp"),
+                    timestamp=_row_timestamp,
                 )
                 msg[_DB_PERSISTED_MARKER] = True
             # The intrinsic markers are now the sole source of truth. Reset the

tests/run_agent/test_run_agent.py

@@ -7151,7 +7151,16 @@ class TestPersistUserMessageOverride:
 
         agent._persist_session(messages, [])
 
-        assert messages[0]["content"] == "Hello there"
+        # The original messages list must NOT be mutated — the persist
+        # override is applied only to the DB row (resolved inside the flush
+        # chokepoint), so the live list keeps the original content for the
+        # API call (#48677).
+        assert (
+            messages[0]["content"]
+            == "[Voice input — respond concisely and conversationally, "
+            "2-3 sentences max. No code blocks or markdown.] Hello there"
+        )
+        # But the DB write must get the override.
         first_db_write = agent._session_db.append_message.call_args_list[0].kwargs
         assert first_db_write["content"] == "Hello there"