Persist Atlas chat history; fix re-greeting on refresh

- GET /api/projects/[id]/atlas-chat returns stored user+assistant messages
- POST handles __atlas_init__ trigger: runs once when no history exists,
  not stored as a user turn so Atlas intro appears cleanly
- Rewrite AtlasChat.tsx: fully self-contained component with own message
  state; loads history from DB on mount, only greets on first open
- Remove assistant-ui runtime dependency for message persistence
- Add Vision & Success Metrics, Integrations & Dependencies, Open Questions
  to PRD section tracker (now 12 sections matching the PDF)

Made-with: Cursor

app/api/projects/[projectId]/atlas-chat/route.ts

@@ -66,6 +66,30 @@ async function savePrd(projectId: string, prdContent: string): Promise<void> {
   }
 }
 
+// ---------------------------------------------------------------------------
+// GET — load stored conversation messages for display
+// ---------------------------------------------------------------------------
+
+export async function GET(
+  _req: NextRequest,
+  { params }: { params: Promise<{ projectId: string }> }
+) {
+  const session = await getServerSession(authOptions);
+  if (!session?.user?.email) {
+    return NextResponse.json({ error: "Unauthorized" }, { status: 401 });
+  }
+
+  const { projectId } = await params;
+  const history = await loadAtlasHistory(projectId);
+
+  // Filter to only user/assistant messages (no system prompts) for display
+  const messages = history
+    .filter((m: any) => m.role === "user" || m.role === "assistant")
+    .map((m: any) => ({ role: m.role as "user" | "assistant", content: m.content as string }));
+
+  return NextResponse.json({ messages });
+}
+
 // ---------------------------------------------------------------------------
 // POST — send message to Atlas
 // ---------------------------------------------------------------------------
@@ -90,14 +114,25 @@ export async function POST(
   // Load conversation history from DB to persist across agent runner restarts
   const history = await loadAtlasHistory(projectId);
 
+  // __init__ is a special internal trigger used only when there is no existing history.
+  // If history already exists, ignore the init request (conversation already started).
+  const isInit = message.trim() === "__atlas_init__";
+  if (isInit && history.length > 0) {
+    return NextResponse.json({ reply: null, alreadyStarted: true });
+  }
+
   try {
     const res = await fetch(`${AGENT_RUNNER_URL}/atlas/chat`, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
       body: JSON.stringify({
-        message,
+        // For init, send the greeting prompt but don't store it as a user message
+        message: isInit
+          ? "Begin the conversation. Introduce yourself as Atlas and ask what the user is building. Do not acknowledge this as an internal trigger."
+          : message,
         session_id: sessionId,
         history,
+        is_init: isInit,
       }),
       signal: AbortSignal.timeout(120_000),
     });