fix(chat): sort messages appropriately

src/components/chat/view/ChatInterface.tsx

@@ -325,6 +325,7 @@ function ChatInterface({
           onWheel={handleScroll}
           onTouchMove={handleScroll}
           isLoadingSessionMessages={isLoadingSessionMessages}
+          isProcessing={isProcessing}
           chatMessages={chatMessages}
           selectedSession={selectedSession}
           currentSessionId={currentSessionId}

src/components/chat/view/subcomponents/ChatMessagesPane.tsx

@@ -19,6 +19,8 @@ interface ChatMessagesPaneProps {
   onWheel: () => void;
   onTouchMove: () => void;
   isLoadingSessionMessages: boolean;
+  /** True while the viewed session has an active provider run in flight. */
+  isProcessing?: boolean;
   chatMessages: ChatMessage[];
   selectedSession: ProjectSession | null;
   currentSessionId: string | null;
@@ -68,6 +70,7 @@ export default function ChatMessagesPane({
   onWheel,
   onTouchMove,
   isLoadingSessionMessages,
+  isProcessing = false,
   chatMessages,
   selectedSession,
   currentSessionId,
@@ -147,7 +150,7 @@ export default function ChatMessagesPane({
       onTouchMove={onTouchMove}
       className="relative flex-1 space-y-3 overflow-y-auto overflow-x-hidden px-0 py-3 sm:space-y-4 sm:p-4"
     >
-      {isLoadingSessionMessages && chatMessages.length === 0 ? (
+      {(isLoadingSessionMessages || isProcessing) && chatMessages.length === 0 ? (
         <div className="mt-8 text-center text-gray-500 dark:text-gray-400">
           <div className="flex items-center justify-center space-x-2">
             <div className="h-4 w-4 animate-spin rounded-full border-b-2 border-gray-400" />

src/stores/useSessionStore.ts

@@ -166,6 +166,108 @@ function hasServerEchoForLocalUser(
   });
 }
 
+function compareMessagesChronologically(a: NormalizedMessage, b: NormalizedMessage): number {
+  const timeA = readMessageTime(a) ?? 0;
+  const timeB = readMessageTime(b) ?? 0;
+  if (timeA !== timeB) {
+    return timeA - timeB;
+  }
+  return 0;
+}
+
+/**
+ * Count how many user turns precede `message` in a chronologically merged view
+ * of server + realtime rows. Used to match a realtime row to the correct turn
+ * on disk when several turns share identical assistant text.
+ */
+function getUserTurnOrdinalBefore(
+  message: NormalizedMessage,
+  serverMessages: NormalizedMessage[],
+  realtimeMessages: NormalizedMessage[],
+): number {
+  const messageTime = readMessageTime(message);
+  let userCount = 0;
+
+  for (const candidate of [...serverMessages, ...realtimeMessages].sort(compareMessagesChronologically)) {
+    if (candidate.id === message.id) {
+      break;
+    }
+
+    const candidateTime = readMessageTime(candidate);
+    if (
+      messageTime !== null
+      && candidateTime !== null
+      && candidateTime > messageTime
+    ) {
+      break;
+    }
+
+    if (candidate.kind === 'text' && candidate.role === 'user') {
+      userCount++;
+    }
+  }
+
+  return Math.max(0, userCount - 1);
+}
+
+function findServerTurnRangeByOrdinal(
+  serverMessages: NormalizedMessage[],
+  turnOrdinal: number,
+): { start: number; end: number } | null {
+  let userCount = -1;
+  let start = -1;
+
+  for (let index = 0; index < serverMessages.length; index++) {
+    const message = serverMessages[index];
+    if (message.kind === 'text' && message.role === 'user') {
+      userCount++;
+      if (userCount === turnOrdinal) {
+        start = index;
+        break;
+      }
+    }
+  }
+
+  if (start < 0) {
+    return null;
+  }
+
+  let end = serverMessages.length;
+  for (let index = start + 1; index < serverMessages.length; index++) {
+    if (serverMessages[index].kind === 'text' && serverMessages[index].role === 'user') {
+      end = index;
+      break;
+    }
+  }
+
+  return { start, end };
+}
+
+function isAssistantTextEchoedInSameTurnOnServer(
+  message: NormalizedMessage,
+  serverMessages: NormalizedMessage[],
+  realtimeMessages: NormalizedMessage[],
+): boolean {
+  const assistantText = (message.content || '').trim();
+  if (!assistantText) {
+    return false;
+  }
+
+  const turnOrdinal = getUserTurnOrdinalBefore(message, serverMessages, realtimeMessages);
+  const turnRange = findServerTurnRangeByOrdinal(serverMessages, turnOrdinal);
+  if (!turnRange) {
+    return false;
+  }
+
+  return serverMessages
+    .slice(turnRange.start + 1, turnRange.end)
+    .some((serverMessage) =>
+      serverMessage.kind === 'text'
+      && serverMessage.role === 'assistant'
+      && (serverMessage.content || '').trim() === assistantText,
+    );
+}
+
 /**
  * After `finalizeStreaming`, the client holds a synthetic assistant `text` row
  * while the sessions API soon returns the same reply with a different id.
@@ -203,22 +305,92 @@ function dedupeAdjacentAssistantEchoes(merged: NormalizedMessage[]): NormalizedM
   return out;
 }
 
+/**
+ * After a server refresh, drop only the realtime rows the persisted transcript
+ * already owns. Anything not yet on disk (common right after `complete`, while
+ * JSONL indexing lags) stays in `realtimeMessages` so the chat pane never
+ * flashes the empty "Continue your conversation" state.
+ */
+function pruneRealtimeSupersededByServer(
+  serverMessages: NormalizedMessage[],
+  realtimeMessages: NormalizedMessage[],
+): NormalizedMessage[] {
+  if (realtimeMessages.length === 0) {
+    return realtimeMessages;
+  }
+
+  const serverIds = new Set(serverMessages.map((message) => message.id));
+
+  return realtimeMessages.filter((message) => {
+    if (serverIds.has(message.id)) {
+      return false;
+    }
+
+    if (message.id.startsWith('local_') && hasServerEchoForLocalUser(message, serverMessages)) {
+      return false;
+    }
+
+    if (message.kind === 'stream_delta' || message.id === `__streaming_${message.sessionId}`) {
+      if (isAssistantTextEchoedInSameTurnOnServer(message, serverMessages, realtimeMessages)) {
+        return false;
+      }
+      return true;
+    }
+
+    if (message.kind === 'text' && message.role === 'assistant') {
+      if (isAssistantTextEchoedInSameTurnOnServer(message, serverMessages, realtimeMessages)) {
+        return false;
+      }
+      return true;
+    }
+
+    if (message.kind === 'text' && message.role === 'user') {
+      return !hasServerEchoForLocalUser(message, serverMessages);
+    }
+
+    if (message.kind === 'tool_use' && message.toolId) {
+      if (serverMessages.some((serverMessage) => serverMessage.kind === 'tool_use' && serverMessage.toolId === message.toolId)) {
+        return false;
+      }
+    }
+
+    return true;
+  });
+}
+
 function computeMerged(server: NormalizedMessage[], realtime: NormalizedMessage[]): NormalizedMessage[] {
-  if (realtime.length === 0) return server;
-  if (server.length === 0) return dedupeAdjacentAssistantEchoes(realtime);
-  const serverIds = new Set(server.map(m => m.id));
-  const extra = realtime.filter((m) => {
-    if (serverIds.has(m.id)) return false;
+  if (realtime.length === 0) {
+    return dedupeAdjacentAssistantEchoes(server);
+  }
+  if (server.length === 0) {
+    return dedupeAdjacentAssistantEchoes(realtime);
+  }
+
+  const serverIds = new Set(server.map((message) => message.id));
+  const extra = realtime.filter((message) => {
+    if (serverIds.has(message.id)) {
+      return false;
+    }
     // Optimistic user rows use `local_*` ids; once the same text exists on the
     // server-backed copy from the same send window, drop the realtime echo to
     // avoid duplicate bubbles without hiding repeated prompts from history.
-    if (m.id.startsWith('local_')) {
-      if (hasServerEchoForLocalUser(m, server)) return false;
+    if (message.id.startsWith('local_')) {
+      if (hasServerEchoForLocalUser(message, server)) {
+        return false;
+      }
     }
     return true;
   });
-  if (extra.length === 0) return server;
-  return dedupeAdjacentAssistantEchoes([...server, ...extra]);
+
+  if (extra.length === 0) {
+    return dedupeAdjacentAssistantEchoes(server);
+  }
+
+  // Interleave by timestamp so live rows stay with their turn instead of
+  // piling up at the bottom after every refresh.
+  return dedupeAdjacentAssistantEchoes(
+    [...server, ...extra].sort(compareMessagesChronologically),
+  );
 }
 
 /**
@@ -439,8 +611,13 @@ export function useSessionStore() {
       slot.total = data.total ?? slot.serverMessages.length;
       slot.hasMore = Boolean(data.hasMore);
       slot.fetchedAt = Date.now();
-      // drop realtime messages that the server has caught up with to prevent unbounded growth.
-      slot.realtimeMessages = [];
+      // Only drop realtime rows the server transcript now owns. A blind clear
+      // here caused the chat pane to flash "Continue your conversation" after
+      // `complete` while JSONL / provider_session_id indexing was still behind.
+      slot.realtimeMessages = pruneRealtimeSupersededByServer(
+        slot.serverMessages,
+        slot.realtimeMessages,
+      );
       recomputeMergedIfNeeded(slot);
       notify(sessionId);
     } catch (error) {