diff --git a/packages/cli/src/notion-page-picker-tui.test.tsx b/packages/cli/src/notion-page-picker-tui.test.tsx
index ae39d39e..2d4dffc3 100644
--- a/packages/cli/src/notion-page-picker-tui.test.tsx
+++ b/packages/cli/src/notion-page-picker-tui.test.tsx
@@ -378,7 +378,7 @@ describe('renderNotionPickerTui', () => {
         },
       ),
     ).resolves.toEqual({ kind: 'quit' });
-    expect(stderr).toContain('Use --no-input --root-page-id <UUID> for scripted mode');
+    expect(stderr).toContain('Use --no-input --notion-root-page-id <UUID> for scripted mode');
     expect(stderr).not.toContain('secret');
   });
 });
diff --git a/packages/cli/src/notion-page-picker-tui.tsx b/packages/cli/src/notion-page-picker-tui.tsx
index fac7f339..30af7522 100644
--- a/packages/cli/src/notion-page-picker-tui.tsx
+++ b/packages/cli/src/notion-page-picker-tui.tsx
@@ -331,7 +331,7 @@ export async function renderNotionPickerTui(
     return result;
   } catch (error) {
     io.stderr.write(
-      `Notion picker requires a TTY. Use --no-input --root-page-id <UUID> for scripted mode. ${sanitizeNotionPickerTuiError(error)}\n`,
+      `Notion picker requires a TTY. Use --no-input --notion-root-page-id <UUID> for scripted mode. ${sanitizeNotionPickerTuiError(error)}\n`,
     );
     return { kind: 'quit' };
   }
diff --git a/packages/cli/src/setup-interrupt.test.ts b/packages/cli/src/setup-interrupt.test.ts
index d8e6350a..62917db6 100644
--- a/packages/cli/src/setup-interrupt.test.ts
+++ b/packages/cli/src/setup-interrupt.test.ts
@@ -17,9 +17,11 @@ function makeTracker(ctrlCValues: boolean[]): SetupInterruptTracker {
 
 describe('setup interrupt confirmation', () => {
   const originalIsTTY = process.stdin.isTTY;
+  const originalRef = process.stdin.ref;
 
   afterEach(() => {
     Object.defineProperty(process.stdin, 'isTTY', { configurable: true, value: originalIsTTY });
+    Object.defineProperty(process.stdin, 'ref', { configurable: true, value: originalRef });
   });
 
   it('fails before opening a prompt when interactive setup has no tty', async () => {
@@ -33,6 +35,26 @@ describe('setup interrupt confirmation', () => {
     expect(prompt).not.toHaveBeenCalled();
   });
 
+  it('refs stdin before opening a real interactive prompt', async () => {
+    const calls: string[] = [];
+    Object.defineProperty(process.stdin, 'isTTY', { configurable: true, value: true });
+    Object.defineProperty(process.stdin, 'ref', {
+      configurable: true,
+      value: vi.fn(() => {
+        calls.push('ref');
+        return process.stdin;
+      }),
+    });
+    const prompt = vi.fn(async () => {
+      calls.push('prompt');
+      return 'continued';
+    });
+
+    await expect(withSetupInterruptConfirmation(prompt)).resolves.toBe('continued');
+
+    expect(calls).toEqual(['ref', 'prompt']);
+  });
+
   it('asks before exiting on Ctrl+C and reruns the active prompt when declined', async () => {
     const prompt = vi.fn(async () => (prompt.mock.calls.length === 1 ? CANCEL : 'continued'));
     const confirmExit = vi.fn(async () => false);
diff --git a/packages/cli/src/setup-interrupt.ts b/packages/cli/src/setup-interrupt.ts
index 5773c336..9baa0f1f 100644
--- a/packages/cli/src/setup-interrupt.ts
+++ b/packages/cli/src/setup-interrupt.ts
@@ -23,6 +23,10 @@ interface SetupInterruptOptions {
 const NON_INTERACTIVE_SETUP_MESSAGE =
   'Interactive setup requires a terminal. Re-run this command in a TTY, or pass --no-input with the required options.';
 
+function refSetupInput(input: NodeJS.ReadStream = stdin): void {
+  input.ref?.();
+}
+
 function createSetupInterruptTracker(input: NodeJS.ReadStream = stdin): SetupInterruptTracker {
   let ctrlCPressed = false;
   const onKeypress = (char: string | undefined, key: Key) => {
@@ -73,6 +77,9 @@ export async function withSetupInterruptConfirmation<T>(
   const confirmExit = options.confirmExit ?? defaultConfirmExit;
 
   while (true) {
+    if (!options.tracker) {
+      refSetupInput();
+    }
     const value = await tracker.track(prompt);
     if (!isCancel(value)) {
       return value;
diff --git a/packages/cli/src/setup-sources.test.ts b/packages/cli/src/setup-sources.test.ts
index b79e43d6..93ad854b 100644
--- a/packages/cli/src/setup-sources.test.ts
+++ b/packages/cli/src/setup-sources.test.ts
@@ -311,6 +311,14 @@ describe('setup sources step', () => {
     ).resolves.toEqual({ status: 'ready', projectDir, connectionIds: ['notion-main'] });
 
     expect(pickNotionRootPages).toHaveBeenCalledOnce();
+    expect(testPrompts.select).toHaveBeenCalledWith({
+      message: 'Which Notion pages should KTX ingest?',
+      options: [
+        { value: 'selected_roots', label: 'Specific pages and their subpages (choose them in a picker)' },
+        { value: 'all_accessible', label: 'All pages the integration can access' },
+        { value: 'back', label: 'Back' },
+      ],
+    });
     expect((await readConfig()).connections['notion-main']).toMatchObject({
       driver: 'notion',
       auth_token_ref: 'env:NOTION_TOKEN',
diff --git a/packages/cli/src/setup-sources.ts b/packages/cli/src/setup-sources.ts
index 5fa4c4af..313dfbe0 100644
--- a/packages/cli/src/setup-sources.ts
+++ b/packages/cli/src/setup-sources.ts
@@ -1270,7 +1270,7 @@ async function promptForInteractiveSource(
       const crawlMode = await prompts.select({
         message: 'Which Notion pages should KTX ingest?',
         options: [
-          { value: 'selected_roots', label: 'Specific pages and their subpages (you\'ll paste page IDs)' },
+          { value: 'selected_roots', label: 'Specific pages and their subpages (choose them in a picker)' },
           { value: 'all_accessible', label: 'All pages the integration can access' },
           { value: 'back', label: 'Back' },
         ],