fix: rebuild session history for undo and segment only new messages

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-opencode)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/mnemosyne/gateway.py

@@ -1469,10 +1469,19 @@ def create_app(
             min_evict_size=min_evict_size,
         )
         _bytes_saved += ingest.bytes_saved
-        if ingest.new_count > 0 or ingest.compacted_count > 0:
+        if ingest.physical_tail_deleted > 0:
+            session._segmented_objects = [
+                obj
+                for obj in session._segmented_objects
+                if obj.turn_end < ingest.deleted_physical_start
+            ]
+
+        if ingest.new_count > 0 or ingest.compacted_count > 0 or ingest.physical_tail_deleted > 0:
             parts = []
             if ingest.new_count:
                 parts.append(f"+{ingest.new_count} msgs")
+            if ingest.physical_tail_deleted:
+                parts.append(f"undo removed {ingest.physical_tail_deleted} msgs")
             if ingest.compacted_count:
                 parts.append(f"{ingest.compacted_count} evicted")
             if ingest.bytes_saved:
@@ -1486,17 +1495,21 @@ def create_app(
                 file=sys.stderr,
             )
 
-        # 1b. Segment new messages into semantic objects and store in ObjectStore
+        # 1b. Segment only newly ingested physical messages into semantic objects
-        #     Phase 4d: admission control gates each object before storage
+        #     and store them in ObjectStore. Re-segmenting the full history here
+        #     would balloon object counts across turns.
         try:
+            if ingest.new_count > 0:
+                new_physical_messages = ms.messages[
+                    ingest.new_physical_start : ingest.new_physical_start + ingest.new_count
+                ]
                 with Timer(session.benchmark.latency["segmentation"]):
                     segmented = session.segmenter.segment_incremental(
-                    ms.messages,
+                        new_physical_messages,
                         session._segmented_objects,
-                    start_turn=0,
+                        start_turn=ingest.new_physical_start,
                     )
                 new_count = len(segmented) - len(session._segmented_objects)
-            if new_count > 0:
                 new_objects = segmented[len(session._segmented_objects) :]
                 admitted_count = 0
                 rejected_count = 0

src/mnemosyne/message_store.py

@@ -79,9 +79,13 @@ def _fingerprint(msg: dict) -> str:
 @dataclass
 class IngestResult:
     """Result of ingesting a new turn's messages."""
+
     new_count: int = 0
+    new_physical_start: int = 0
     mutations_detected: int = 0
     deletions_detected: int = 0
+    physical_tail_deleted: int = 0
+    deleted_physical_start: int = 0
     compacted_count: int = 0
     bytes_saved: int = 0
 
@@ -89,8 +93,7 @@ class IngestResult:
 class MessageStore:
     """Pichay's compacted conversation history for a session."""
 
-    def __init__(self, session_id: str, page_store: PageStore,
+    def __init__(self, session_id: str, page_store: PageStore, log_path: Path | None = None):
-                 log_path: Path | None = None):
         self.session_id = session_id
         self.page_store = page_store
         self.log_path = log_path
@@ -124,10 +127,16 @@ class MessageStore:
             return json.dumps(content, default=str)[:limit]
         return str(content)[:limit]
 
-    def _log_violation(self, kind: str, index: int, msg: dict | None,
+    def _log_violation(
-                       expected_fp: str, actual_fp: str,
+        self,
+        kind: str,
+        index: int,
+        msg: dict | None,
+        expected_fp: str,
+        actual_fp: str,
         old_msg: dict | None = None,
-                       deleted_msgs: list[dict] | None = None) -> None:
+        deleted_msgs: list[dict] | None = None,
+    ) -> None:
         """Log append-only violations to file for later analysis."""
         if self.log_path is None:
             return
@@ -188,20 +197,26 @@ class MessageStore:
         self._turn += 1
         result = IngestResult()
         client_known = len(self._client_fps)
+        first_mutation_index: int | None = None
 
         # ── Detect mutations in known client messages ────────────
         check_limit = min(client_known, len(incoming))
         for i in range(check_limit):
             fp = _fingerprint(incoming[i])
             if fp != self._client_fps[i]:
+                if first_mutation_index is None:
+                    first_mutation_index = i
                 result.mutations_detected += 1
                 self.total_mutations += 1
                 # Look up physical message via mapping for comparison
                 phys_idx = self._client_to_physical[i]
                 old_msg = self._messages[phys_idx] if phys_idx < len(self._messages) else None
                 self._log_violation(
-                    "mutation", i, incoming[i],
+                    "mutation",
-                    self._client_fps[i], fp,
+                    i,
+                    incoming[i],
+                    self._client_fps[i],
+                    fp,
                     old_msg=old_msg,
                 )
                 print(
@@ -210,8 +225,28 @@ class MessageStore:
                     f"got {fp[:32]}{_RESET}",
                     file=sys.stderr,
                 )
-                # Update CLIENT fingerprint only — physical store unchanged
+
-                self._client_fps[i] = fp
+        # Tail mutation: rebuild physical/client history from first changed index onward.
+        if first_mutation_index is not None:
+            if first_mutation_index < len(self._client_to_physical):
+                physical_start = self._client_to_physical[first_mutation_index]
+            else:
+                physical_start = len(self._messages)
+            physical_start = max(0, min(physical_start, len(self._messages)))
+            removed = len(self._messages) - physical_start
+            self._messages = self._messages[:physical_start]
+            self._fingerprints = self._fingerprints[:physical_start]
+            self._client_fps = self._client_fps[:first_mutation_index]
+            self._client_to_physical = self._client_to_physical[:first_mutation_index]
+            client_known = len(self._client_fps)
+            result.physical_tail_deleted = max(result.physical_tail_deleted, removed)
+            result.deleted_physical_start = physical_start
+            print(
+                f"  {_DIM}[{self.session_id}] CLIENT TAIL MUTATION APPLIED: "
+                f"rebuilt history from client index {first_mutation_index} "
+                f"(removed {removed} physical msgs){_RESET}",
+                file=sys.stderr,
+            )
 
         # ── Detect client deletions (compaction) ─────────────────
         if len(incoming) < client_known:
@@ -219,6 +254,7 @@ class MessageStore:
             result.deletions_detected = deleted
             self.total_deletions += deleted
             self.total_client_deletions_absorbed += deleted
+            undo_applied = False
             # Log what the client is deleting (from physical store via mapping)
             deleted_physical = []
             for ci in range(len(incoming), client_known):
@@ -226,24 +262,49 @@ class MessageStore:
                 if pi < len(self._messages):
                     deleted_physical.append(self._messages[pi])
             self._log_violation(
-                "deletion", client_known, None,
+                "deletion",
-                f"expected_{client_known}", f"got_{len(incoming)}",
+                client_known,
+                None,
+                f"expected_{client_known}",
+                f"got_{len(incoming)}",
                 deleted_msgs=deleted_physical,
             )
+            deleted_indices = self._client_to_physical[len(incoming) : client_known]
+            if deleted_indices:
+                valid_deleted = sorted(
+                    {pi for pi in deleted_indices if 0 <= pi < len(self._messages)}
+                )
+                if valid_deleted:
+                    tail_start = valid_deleted[0]
+                    removed = len(self._messages) - tail_start
+                    self._messages = self._messages[:tail_start]
+                    self._fingerprints = self._fingerprints[:tail_start]
+                    result.physical_tail_deleted = removed
+                    result.deleted_physical_start = tail_start
+                    undo_applied = True
+                    print(
+                        f"  {_DIM}[{self.session_id}] CLIENT UNDO APPLIED: "
+                        f"removed {removed} tail messages from physical store{_RESET}",
+                        file=sys.stderr,
+                    )
+
+            if not undo_applied:
                 print(
                     f"  {_DIM}[{self.session_id}] CLIENT DELETION ABSORBED: "
                     f"{deleted} messages dropped by client, "
                     f"physical store unchanged ({len(self._messages)} msgs){_RESET}",
                     file=sys.stderr,
                 )
+
             # Truncate CLIENT tracking only — physical store stays intact
-            self._client_fps = self._client_fps[:len(incoming)]
+            self._client_fps = self._client_fps[: len(incoming)]
-            self._client_to_physical = self._client_to_physical[:len(incoming)]
+            self._client_to_physical = self._client_to_physical[: len(incoming)]
 
         # ── Extract and append new messages ──────────────────────
         new_start = min(client_known, len(incoming))
         new_messages = incoming[new_start:]
         result.new_count = len(new_messages)
+        result.new_physical_start = len(self._messages)
 
         if new_messages:
             # Deep copy new messages so we own them
@@ -256,7 +317,7 @@ class MessageStore:
                 _strip_cache_control(msg)
 
             # Track in physical store and client mapping
-            phys_start = len(self._messages)
+            phys_start = result.new_physical_start
             for j, msg in enumerate(new_messages):
                 fp = _fingerprint(msg)
                 self._fingerprints.append(fp)