diff --git a/.changeset/remove-init-prompts.md b/.changeset/remove-init-prompts.md
new file mode 100644
index 00000000..e2afdc3b
--- /dev/null
+++ b/.changeset/remove-init-prompts.md
@@ -0,0 +1,5 @@
+---
+"clerk": minor
+---
+
+Remove `clerk init --prompt` and the bundled per-framework agent prompt templates. Agents should run `clerk init -y` to perform the full setup non-interactively, or run `skills add clerk/skills` directly via their preferred package runner. The internal `pmInstallCommand` helper has moved from `commands/init/prompts/` to `lib/package-manager.ts`.
diff --git a/packages/cli-core/src/cli-program.ts b/packages/cli-core/src/cli-program.ts
index 6266fb01..30e16d50 100644
--- a/packages/cli-core/src/cli-program.ts
+++ b/packages/cli-core/src/cli-program.ts
@@ -131,7 +131,6 @@ Give AI agents better Clerk context: install the Clerk skills
     )
     .option("--name <project-name>", "Project name for --starter (skips prompt)")
     .option("--app <id>", "Application ID to link (skips interactive picker)")
-    .option("--prompt", "Output a prompt for an AI agent to integrate Clerk")
     .option("--starter", "Create a new project from a starter template")
     .option("-y, --yes", "Skip confirmation prompts")
     .option("--no-skills", "Skip the optional agent skills install prompt")
@@ -150,7 +149,6 @@ Give AI agents better Clerk context: install the Clerk skills
         command: "clerk init --starter --framework next --pm bun",
         description: "Bootstrap with Bun",
       },
-      { command: "clerk init --prompt", description: "Output a setup prompt for an AI agent" },
       { command: "clerk init -y", description: "Skip all confirmation prompts" },
       { command: "clerk init --no-skills", description: "Skip the agent skills install prompt" },
     ])
diff --git a/packages/cli-core/src/commands/init/README.md b/packages/cli-core/src/commands/init/README.md
index 8cdea2d5..3e0c71c6 100644
--- a/packages/cli-core/src/commands/init/README.md
+++ b/packages/cli-core/src/commands/init/README.md
@@ -11,7 +11,6 @@ clerk init --framework next
 clerk init --starter
 clerk init --starter --framework next --pm bun
 clerk init --starter --framework next --pm bun --name my-app
-clerk init --prompt
 clerk init -y
 clerk init --yes
 clerk init --no-skills
@@ -26,7 +25,6 @@ clerk init --no-skills
 | `--name <project-name>` | Project name for `--starter` (skips prompt). Must be lowercase, no spaces, no path separators                                                                                         |
 | `--app <id>`            | Application ID to link (skips the interactive app picker during authenticated linking)                                                                                                |
 | `--starter`             | Bootstrap a new project from a starter template (runs the framework generator, installs deps, and scaffolds Clerk)                                                                    |
-| `--prompt`              | Output a prompt for an AI agent to integrate Clerk, then exit                                                                                                                         |
 | `-y, --yes`             | Skip confirmation prompts (also skips authentication after bootstrap, letting you connect your account later)                                                                         |
 | `--no-skills`           | Skip the optional agent skills install prompt at the end of init                                                                                                                      |
 
@@ -39,31 +37,28 @@ When running in agent mode (`--mode agent` or non-TTY), the command runs the ful
 - For **new projects** (`--starter` or blank directory): `--framework` is required (no way to auto-detect in an empty dir). Package manager is auto-selected by availability (bun → pnpm → yarn → npm) unless `--pm` is provided
 - Project name defaults to the framework's default (e.g. `my-clerk-next-app`) unless `--name` is provided
 
-Use `--prompt` to output a setup prompt for an AI agent without running init.
-
 ## Flow
 
-1. **`--prompt`**: outputs a framework-specific prompt, then exits
-2. Gathers project context (framework, router variant, TypeScript, `src/` directory, package manager)
-3. Determines auth mode from credential presence (no user prompt):
+1. Gathers project context (framework, router variant, TypeScript, `src/` directory, package manager)
+2. Determines auth mode from credential presence (no user prompt):
    - **Authenticated** (OAuth token or `CLERK_PLATFORM_API_KEY` set): uses the authenticated flow — runs `clerk link` if not already linked and pulls real API keys into `.env` at the end
    - **Bootstrap + keyless-capable framework + not authenticated**: automatically uses keyless mode — the app runs on auto-generated dev keys and the user can connect a Clerk account later with `clerk auth login`
    - **Bootstrap + non-keyless framework + not authenticated** (with `--yes` or agent mode): skips authentication and prints manual setup instructions (run `clerk auth login` / `clerk link` / `clerk env pull` when ready)
    - **Existing project + not authenticated**: runs the authenticated flow, which triggers an interactive login so real keys can be pulled
-4. **Authenticated mode only**: authenticates via `clerk auth login` (skipped if already authenticated) and links the project via `clerk link` (skipped if already linked)
-5. Displays detected framework and variant
-6. Detects existing auth libraries (NextAuth, Auth0, Supabase, Firebase, Passport, Better Auth, Kinde) and shows migration guidance
-7. Installs the appropriate Clerk SDK (skips if already present)
-8. Generates a scaffold plan for the detected framework
-9. Warns if the git working tree has uncommitted changes
-10. Previews planned file changes and asks for confirmation
-11. Writes scaffold files to disk
-12. Runs project formatters (Prettier/Biome) on generated files
-13. Scans for issues: hardcoded keys, leftover auth-library imports, stale API calls
-14. Prints a summary of created, modified, and skipped files with recommendations
-15. **Authenticated mode**: pulls development instance API keys via `clerk env pull`
-16. **Unauthenticated mode**: prints instructions for development without API keys and how to connect a Clerk account later
-17. Optionally installs Clerk agent skills (core + features, plus a framework-specific skill) via the project's package runner (see [Agent skills install](#agent-skills-install))
+3. **Authenticated mode only**: authenticates via `clerk auth login` (skipped if already authenticated) and links the project via `clerk link` (skipped if already linked)
+4. Displays detected framework and variant
+5. Detects existing auth libraries (NextAuth, Auth0, Supabase, Firebase, Passport, Better Auth, Kinde) and shows migration guidance
+6. Installs the appropriate Clerk SDK (skips if already present)
+7. Generates a scaffold plan for the detected framework
+8. Warns if the git working tree has uncommitted changes
+9. Previews planned file changes and asks for confirmation
+10. Writes scaffold files to disk
+11. Runs project formatters (Prettier/Biome) on generated files
+12. Scans for issues: hardcoded keys, leftover auth-library imports, stale API calls
+13. Prints a summary of created, modified, and skipped files with recommendations
+14. **Authenticated mode**: pulls development instance API keys via `clerk env pull`
+15. **Unauthenticated mode**: prints instructions for development without API keys and how to connect a Clerk account later
+16. Optionally installs Clerk agent skills (core + features, plus a framework-specific skill) via the project's package runner (see [Agent skills install](#agent-skills-install))
 
 ## Framework Detection
 
@@ -185,7 +180,6 @@ After scaffolding (and after env keys are pulled or keyless instructions are pri
 
 - **Human mode**: prompts `Install agent skills? (...)` defaulting to yes. Pass `--no-skills` to suppress the prompt entirely, or `-y/--yes` to accept it without confirmation. When more than one runner is available, a second prompt picks which one to use (the project's package manager wins by default).
 - **Agent mode**: skills are installed non-interactively with `-y -g` flags (no prompt shown). Pass `--no-skills` to skip entirely.
-- **`--prompt`**: exits before the skills step runs. Agent users should run `skills add clerk/skills` via their preferred runner manually; the bundled `clerk` skill is only installable via `clerk init` itself, since its source lives inside the CLI binary.
 
 Two install commands run, sharing one runner:
 
diff --git a/packages/cli-core/src/commands/init/heuristics.ts b/packages/cli-core/src/commands/init/heuristics.ts
index d6fdb4fc..fab992ba 100644
--- a/packages/cli-core/src/commands/init/heuristics.ts
+++ b/packages/cli-core/src/commands/init/heuristics.ts
@@ -6,7 +6,7 @@ import { log } from "../../lib/log.js";
 import { getValidToken, hasStoredCredentials } from "../../lib/credential-store.js";
 import { fetchUserInfo } from "../../lib/token-exchange.js";
 import { printFindings } from "./scan.js";
-import { pmInstallCommand } from "./prompts/index.js";
+import { pmInstallCommand } from "../../lib/package-manager.js";
 import { withSpinner } from "../../lib/spinner.js";
 import type { FileAction, ProjectContext, ScaffoldPlan } from "./frameworks/types.js";
 import type { ScanFinding } from "./scan.js";
diff --git a/packages/cli-core/src/commands/init/index.test.ts b/packages/cli-core/src/commands/init/index.test.ts
index 2f05a203..bc32b697 100644
--- a/packages/cli-core/src/commands/init/index.test.ts
+++ b/packages/cli-core/src/commands/init/index.test.ts
@@ -169,16 +169,6 @@ describe("init", () => {
     expect(bootstrapMod.promptAndBootstrap).not.toHaveBeenCalled();
   });
 
-  test("--prompt flag prints guidance and exits", async () => {
-    const { captured } = setup({ isAgent: false });
-
-    await captured.run(() => init({ prompt: true }));
-
-    expect(captured.out).toContain("clerk init -y");
-    expect(loginMod.login).not.toHaveBeenCalled();
-    expect(bootstrapMod.promptAndBootstrap).not.toHaveBeenCalled();
-  });
-
   test("blank dir in human mode triggers bootstrap flow", async () => {
     setup();
     setupBootstrapSuccess();
diff --git a/packages/cli-core/src/commands/init/index.ts b/packages/cli-core/src/commands/init/index.ts
index 79e35ace..e69908d1 100644
--- a/packages/cli-core/src/commands/init/index.ts
+++ b/packages/cli-core/src/commands/init/index.ts
@@ -46,8 +46,6 @@ type InitOptions = {
   pm?: PackageManager;
   name?: string;
   yes?: boolean;
-  /** Output a prompt for an AI agent to integrate Clerk, then exit. */
-  prompt?: boolean;
   /** Install the optional agent skills (set to false via `--no-skills` to skip). */
   skills?: boolean;
   /** Create a new project from a starter template. */
@@ -63,13 +61,6 @@ export async function init(options: InitOptions = {}) {
     ? (lookupFramework(options.framework) ?? undefined)
     : undefined;
 
-  if (options.prompt) {
-    log.data(
-      "Run `clerk init -y` to automatically detect the framework, install the Clerk SDK, and scaffold authentication files without interactive prompts.",
-    );
-    return;
-  }
-
   // In agent mode, implicitly enable --yes to skip all confirmation prompts.
   const overrides: BootstrapOverrides = {
     skipConfirm: options.yes || isAgent(),
diff --git a/packages/cli-core/src/commands/init/prompts/astro.md b/packages/cli-core/src/commands/init/prompts/astro.md
deleted file mode 100644
index 2702e735..00000000
--- a/packages/cli-core/src/commands/init/prompts/astro.md
+++ /dev/null
@@ -1,113 +0,0 @@
-# Add Clerk to Astro
-
-Install `{{SDK}}`. Add `clerk()` integration to `astro.config.mjs`. Create middleware with `clerkMiddleware()`. Use `<Show>`, `<SignIn>`, `<SignUp>`, `<UserButton>` from `@clerk/astro/components`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## astro.config.mjs
-
-```typescript
-import { defineConfig } from "astro/config";
-import clerk from "@clerk/astro";
-
-export default defineConfig({
-  integrations: [clerk()],
-  output: "server",
-});
-```
-
-## src/middleware.ts
-
-```typescript
-import { clerkMiddleware } from "@clerk/astro/server";
-
-export const onRequest = clerkMiddleware();
-```
-
-## src/pages/sign-in.astro
-
-```astro
----
-import { SignIn } from '@clerk/astro/components';
----
-<SignIn />
-```
-
-## src/pages/sign-up.astro
-
-```astro
----
-import { SignUp } from '@clerk/astro/components';
----
-<SignUp />
-```
-
-## Example usage in a layout
-
-```astro
----
-import { Show, SignInButton, SignUpButton, UserButton } from '@clerk/astro/components';
----
-<header>
-  <Show when="signed-out">
-    <SignInButton />
-    <SignUpButton />
-  </Show>
-  <Show when="signed-in">
-    <UserButton />
-  </Show>
-</header>
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Add `clerk()` to `integrations` in `astro.config.mjs`
-- Set `output: 'server'` (SSR required) with an SSR adapter
-- Use `clerkMiddleware()` from `@clerk/astro/server` in `src/middleware.ts`
-- Import components from `@clerk/astro/components`
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Import from `@clerk/react` or `@clerk/nextjs` — use `@clerk/astro`
-- Skip `output: 'server'` (Clerk requires SSR)
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { authMiddleware } from '@clerk/astro' // WRONG — use clerkMiddleware
-<SignedIn>                                    // WRONG — use <Show when="signed-in">
-<SignedOut>                                   // WRONG — use <Show when="signed-out">
-output: 'static'                              // WRONG — Clerk requires SSR
-```
-
-## Verify Before Responding
-
-1. Is `clerk()` in `integrations` in `astro.config.mjs`?
-2. Is `output: 'server'` set?
-3. Is `clerkMiddleware()` exported as `onRequest` in `src/middleware.ts`?
-4. Are components imported from `@clerk/astro/components`?
-5. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/expo.md b/packages/cli-core/src/commands/init/prompts/expo.md
deleted file mode 100644
index 77d43fb5..00000000
--- a/packages/cli-core/src/commands/init/prompts/expo.md
+++ /dev/null
@@ -1,119 +0,0 @@
-# Add Clerk to Expo
-
-Install `{{SDK}}`. Wrap the app in `<ClerkProvider>` with a secure token cache. Use `<Show>`, `<SignInButton>`, `<SignUpButton>`, `<UserButton>` from `@clerk/expo`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## Token Cache
-
-Create a secure token cache using `expo-secure-store`:
-
-```bash
-{{INSTALL_CMD_EXTRA}}
-```
-
-```typescript
-import * as SecureStore from "expo-secure-store";
-
-export const tokenCache = {
-  async getToken(key: string) {
-    return SecureStore.getItemAsync(key);
-  },
-  async saveToken(key: string, value: string) {
-    return SecureStore.setItemAsync(key, value);
-  },
-  async clearToken(key: string) {
-    return SecureStore.deleteItemAsync(key);
-  },
-};
-```
-
-## App entry (app/\_layout.{{JSX}} or App.{{JSX}})
-
-```typescript
-import { ClerkProvider, ClerkLoaded } from "@clerk/expo";
-import { tokenCache } from "./token-cache";
-
-export default function RootLayout() {
-  const publishableKey = process.env.{{ENV_VAR}};
-
-  return (
-    <ClerkProvider tokenCache={tokenCache} publishableKey={publishableKey}>
-      <ClerkLoaded>
-        {/* your app content */}
-      </ClerkLoaded>
-    </ClerkProvider>
-  );
-}
-```
-
-## Example usage
-
-```typescript
-import { Show, SignInButton, SignUpButton, UserButton } from "@clerk/expo";
-
-export default function Home() {
-  return (
-    <>
-      <Show when="signed-out">
-        <SignInButton />
-        <SignUpButton />
-      </Show>
-      <Show when="signed-in">
-        <UserButton />
-      </Show>
-    </>
-  );
-}
-```
-
-## Environment
-
-Env var (`{{ENV_VAR}}`) is in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `@clerk/expo` (not `@clerk/react` or `@clerk/nextjs`)
-- Pass `tokenCache` to `<ClerkProvider>` for secure token storage
-- Pass `publishableKey` explicitly from `process.env.{{ENV_VAR}}`
-- Wrap content with `<ClerkLoaded>` inside `<ClerkProvider>`
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `@clerk/react` or `@clerk/nextjs` — use `@clerk/expo`
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Skip the `tokenCache` (tokens won't persist across app restarts)
-- Use `localStorage` or `AsyncStorage` directly for tokens
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { ClerkProvider } from "@clerk/react"   // WRONG — use @clerk/expo
-<SignedIn>                                     // WRONG — use <Show when="signed-in">
-<SignedOut>                                    // WRONG — use <Show when="signed-out">
-```
-
-## Verify Before Responding
-
-1. Is `@clerk/expo` used (not `@clerk/react`)?
-2. Is `tokenCache` passed to `<ClerkProvider>`?
-3. Is `<ClerkLoaded>` wrapping the app content?
-4. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/express.md b/packages/cli-core/src/commands/init/prompts/express.md
deleted file mode 100644
index 7ef0893c..00000000
--- a/packages/cli-core/src/commands/init/prompts/express.md
+++ /dev/null
@@ -1,78 +0,0 @@
-# Add Clerk to Express
-
-Install `{{SDK}}`. Add `clerkMiddleware()` to the Express app. Use `requireAuth()` to protect routes. Use `getAuth()` to access auth state in handlers.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## Server setup
-
-```typescript
-import express from "express";
-import { clerkMiddleware, requireAuth, getAuth } from "@clerk/express";
-
-const app = express();
-
-// Apply Clerk middleware to all routes
-app.use(clerkMiddleware());
-
-// Public route — no auth required
-app.get("/", (req, res) => {
-  res.json({ message: "Public route" });
-});
-
-// Protected route — requires authentication
-app.get("/protected", requireAuth(), (req, res) => {
-  const { userId } = getAuth(req);
-  res.json({ userId });
-});
-
-app.listen(3000);
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `clerkMiddleware()` from `@clerk/express` as Express middleware
-- Use `requireAuth()` to protect routes that need authentication
-- Use `getAuth(req)` to access auth state (`userId`, `sessionId`, etc.)
-- Apply `clerkMiddleware()` before any route that needs auth
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `@clerk/nextjs` or `@clerk/react` — use `@clerk/express`
-- Use deprecated `ClerkExpressRequireAuth` or `ClerkExpressWithAuth` (replaced by `requireAuth` and `getAuth`)
-- Skip `clerkMiddleware()` — it's required for `requireAuth()` and `getAuth()` to work
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { ClerkExpressRequireAuth } from "@clerk/express"; // WRONG — use requireAuth
-import { ClerkExpressWithAuth } from "@clerk/express"; // WRONG — use clerkMiddleware + getAuth
-```
-
-## Verify Before Responding
-
-1. Is `clerkMiddleware()` applied as middleware?
-2. Are protected routes using `requireAuth()`?
-3. Is `getAuth(req)` used to access auth state (not `req.auth` directly)?
-4. Are imports from `@clerk/express`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user test the protected route by sending a request without authentication (should get 401) and with a valid session token (should succeed). Then recommend exploring: Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/fastify.md b/packages/cli-core/src/commands/init/prompts/fastify.md
deleted file mode 100644
index a9c712ac..00000000
--- a/packages/cli-core/src/commands/init/prompts/fastify.md
+++ /dev/null
@@ -1,78 +0,0 @@
-# Add Clerk to Fastify
-
-Install `{{SDK}}`. Register `clerkPlugin` with the Fastify instance. Use `getAuth()` to access auth state in handlers.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## Server setup
-
-```typescript
-import Fastify from "fastify";
-import { clerkPlugin, getAuth } from "@clerk/fastify";
-
-const fastify = Fastify();
-
-// Register Clerk plugin
-fastify.register(clerkPlugin);
-
-// Public route — no auth required
-fastify.get("/", async (request, reply) => {
-  return { message: "Public route" };
-});
-
-// Protected route — check auth in handler
-fastify.get("/protected", async (request, reply) => {
-  const { userId } = getAuth(request);
-  if (!userId) {
-    return reply.code(401).send({ error: "Unauthorized" });
-  }
-  return { userId };
-});
-
-fastify.listen({ port: 3000 });
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Register `clerkPlugin` from `@clerk/fastify` with `fastify.register()`
-- Use `getAuth(request)` to access auth state (`userId`, `sessionId`, etc.)
-- Register the plugin before defining routes that need auth
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `@clerk/nextjs` or `@clerk/express` — use `@clerk/fastify`
-- Use deprecated `clerkPreHandler` (replaced by `clerkPlugin` + `getAuth`)
-- Skip `clerkPlugin` registration — it's required for `getAuth()` to work
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { clerkPreHandler } from "@clerk/fastify"; // WRONG — use clerkPlugin + getAuth
-```
-
-## Verify Before Responding
-
-1. Is `clerkPlugin` registered with `fastify.register()`?
-2. Is `getAuth(request)` used to access auth state?
-3. Are imports from `@clerk/fastify`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user test the protected route by sending a request without authentication (should get 401) and with a valid session token (should succeed). Then recommend exploring: Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/generic-fallback.md b/packages/cli-core/src/commands/init/prompts/generic-fallback.md
deleted file mode 100644
index f82ea61d..00000000
--- a/packages/cli-core/src/commands/init/prompts/generic-fallback.md
+++ /dev/null
@@ -1,49 +0,0 @@
-# Add Clerk to {{FRAMEWORK_NAME}}
-
-Install `{{SDK}}`. Set up the Clerk provider/middleware for {{FRAMEWORK_NAME}}. Use `<Show>` for conditional auth rendering.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## Steps
-
-1. Set up the Clerk provider/middleware for {{FRAMEWORK_NAME}}.
-2. Create sign-in and sign-up routes/components.
-3. Use `<Show when="signed-in">` and `<Show when="signed-out">` for conditional rendering.
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `{{SDK}}` — the correct SDK for {{FRAMEWORK_NAME}}
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Import from the wrong Clerk SDK package
-
-## Verify Before Responding
-
-1. Is `{{SDK}}` installed?
-2. Is the Clerk provider wrapping the application?
-3. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/generic.md b/packages/cli-core/src/commands/init/prompts/generic.md
deleted file mode 100644
index 84fb01a6..00000000
--- a/packages/cli-core/src/commands/init/prompts/generic.md
+++ /dev/null
@@ -1,44 +0,0 @@
-# Add Clerk Authentication
-
-Integrate Clerk auth into this project. Use the Clerk SDK appropriate for the project's framework.
-
-Latest docs: https://clerk.com/docs
-
-## Steps
-
-1. Authenticate with Clerk: Run `clerk auth login` to log in via the browser.
-2. Link a Clerk application: Run `clerk link` to associate this directory with a Clerk application.
-3. Install the Clerk SDK appropriate for the project's framework (see https://clerk.com/docs).
-4. Pull environment variables with `clerk env pull`.
-5. Set up the Clerk provider at the root of the application.
-6. Add sign-in and sign-up routes/components.
-7. Protect routes that require authentication.
-
-## Rules
-
-ALWAYS:
-
-- Use the framework-specific Clerk SDK (e.g. `@clerk/nextjs`, `@clerk/react`, `@clerk/vue`)
-- Use `<Show>` for conditional rendering based on auth state
-- Use existing package manager
-- Follow the framework-specific quickstart at https://clerk.com/docs
-
-NEVER:
-
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Use `frontendApi` (removed, use `publishableKey` env var)
-
-## Verify Before Responding
-
-1. Is the correct framework-specific Clerk SDK installed?
-2. Is the Clerk provider wrapping the application root?
-3. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/index.ts b/packages/cli-core/src/commands/init/prompts/index.ts
deleted file mode 100644
index 1dc36bbc..00000000
--- a/packages/cli-core/src/commands/init/prompts/index.ts
+++ /dev/null
@@ -1,160 +0,0 @@
-import type { ProjectContext } from "../frameworks/types.js";
-import { jsxExt, scriptExt, srcPrefix } from "../frameworks/helpers.js";
-
-// Static text imports — embedded at build time, safe for compiled binaries.
-import genericMd from "./generic.md" with { type: "text" };
-import genericFallbackMd from "./generic-fallback.md" with { type: "text" };
-import nextjsAppRouterMd from "./nextjs-app-router.md" with { type: "text" };
-import nextjsPagesRouterMd from "./nextjs-pages-router.md" with { type: "text" };
-import reactMd from "./react.md" with { type: "text" };
-import reactRouterMd from "./react-router.md" with { type: "text" };
-import nuxtMd from "./nuxt.md" with { type: "text" };
-import tanstackStartMd from "./tanstack-start.md" with { type: "text" };
-import astroMd from "./astro.md" with { type: "text" };
-import vueMd from "./vue.md" with { type: "text" };
-import expoMd from "./expo.md" with { type: "text" };
-import expressMd from "./express.md" with { type: "text" };
-import fastifyMd from "./fastify.md" with { type: "text" };
-
-const TEMPLATES = {
-  generic: genericMd,
-  "generic-fallback": genericFallbackMd,
-  "nextjs-app-router": nextjsAppRouterMd,
-  "nextjs-pages-router": nextjsPagesRouterMd,
-  react: reactMd,
-  "react-router": reactRouterMd,
-  nuxt: nuxtMd,
-  "tanstack-start": tanstackStartMd,
-  astro: astroMd,
-  vue: vueMd,
-  expo: expoMd,
-  express: expressMd,
-  fastify: fastifyMd,
-} satisfies Record<string, string>;
-
-type TemplateName = keyof typeof TEMPLATES;
-type FrameworkTemplateName = Exclude<TemplateName, "generic">;
-type FrameworkPromptInfo = { template: FrameworkTemplateName; docsUrl: string };
-
-function loadTemplate(name: TemplateName): string {
-  const template = TEMPLATES[name];
-  // The project formatter escapes underscores in markdown headings (e.g. `_app` → `\_app`).
-  // These templates are output as plain text, so undo that escaping.
-  return template.replaceAll("\\_", "_");
-}
-
-function interpolate(template: string, vars: Record<string, string>): string {
-  return template.replace(/\{\{(\w+)\}\}/g, (_, key) => vars[key] ?? `{{${key}}}`);
-}
-
-const PM_COMMANDS = {
-  bun: "bun add",
-  yarn: "yarn add",
-  pnpm: "pnpm add",
-  npm: "npm install",
-} satisfies Record<ProjectContext["packageManager"], string>;
-
-export function pmInstallCommand(pm: ProjectContext["packageManager"]): string {
-  return PM_COMMANDS[pm];
-}
-
-// Maps framework dep to its template filename and docs URL.
-// Next.js defaults to app-router; pages-router variant is handled in resolveTemplate.
-const FRAMEWORK_PROMPTS: Record<string, FrameworkPromptInfo> = {
-  next: {
-    template: "nextjs-app-router",
-    docsUrl: "https://clerk.com/docs/nextjs/getting-started/quickstart",
-  },
-  react: { template: "react", docsUrl: "https://clerk.com/docs/react/getting-started/quickstart" },
-  "react-router": {
-    template: "react-router",
-    docsUrl: "https://clerk.com/docs/react-router/getting-started/quickstart",
-  },
-  nuxt: { template: "nuxt", docsUrl: "https://clerk.com/docs/nuxt/getting-started/quickstart" },
-  "@tanstack/react-start": {
-    template: "tanstack-start",
-    docsUrl: "https://clerk.com/docs/tanstack-start/getting-started/quickstart",
-  },
-  astro: { template: "astro", docsUrl: "https://clerk.com/docs/astro/getting-started/quickstart" },
-  vue: { template: "vue", docsUrl: "https://clerk.com/docs/vue/getting-started/quickstart" },
-  vite: {
-    template: "generic-fallback",
-    docsUrl: "https://clerk.com/docs/js-frontend/getting-started/quickstart",
-  },
-  expo: { template: "expo", docsUrl: "https://clerk.com/docs/expo/getting-started/quickstart" },
-  express: {
-    template: "express",
-    docsUrl: "https://clerk.com/docs/express/getting-started/quickstart",
-  },
-  fastify: {
-    template: "fastify",
-    docsUrl: "https://clerk.com/docs/fastify/getting-started/quickstart",
-  },
-};
-
-const DEFAULT_DOCS_URL = "https://clerk.com/docs";
-
-type RequiredPromptVar =
-  | "SDK"
-  | "ENV_VAR"
-  | "INSTALL_CMD"
-  | "BASE"
-  | "BASE_DISPLAY"
-  | "EXT"
-  | "JSX"
-  | "MIDDLEWARE_BASENAME"
-  | "LAYOUT_PATH"
-  | "ENV_FILE"
-  | "PM"
-  | "DOCS_URL"
-  | "FRAMEWORK_NAME";
-
-type OptionalPromptVar = "INSTALL_CMD_EXTRA";
-type PromptVars = Record<RequiredPromptVar, string> & Partial<Record<OptionalPromptVar, string>>;
-
-// NOTE: The agent prompts show simple `clerkMiddleware()` (matching official docs).
-// The scaffold code in `frameworks/helpers.ts` uses `createRouteMatcher` + `auth.protect()`
-// which is more opinionated. This divergence is intentional — agents should follow the
-// docs pattern; scaffolded code provides a production-ready starting point.
-
-function buildVars(ctx: ProjectContext): PromptVars {
-  const base = srcPrefix(ctx);
-  const ext = scriptExt(ctx);
-  const jsx = jsxExt(ctx);
-  const installCmd = `${pmInstallCommand(ctx.packageManager)} ${ctx.framework.sdk}`;
-
-  const vars: PromptVars = {
-    SDK: ctx.framework.sdk,
-    ENV_VAR: ctx.framework.envVar,
-    INSTALL_CMD: installCmd,
-    BASE: base,
-    BASE_DISPLAY: base || "project root",
-    EXT: ext,
-    JSX: jsx,
-    MIDDLEWARE_BASENAME: ctx.middlewareBasename ?? "proxy",
-    LAYOUT_PATH: ctx.layoutPath ?? `${base}app/layout.${jsx}`,
-    ENV_FILE: ctx.envFile,
-    PM: ctx.packageManager,
-    DOCS_URL: FRAMEWORK_PROMPTS[ctx.framework.dep]?.docsUrl ?? DEFAULT_DOCS_URL,
-    FRAMEWORK_NAME: ctx.framework.name,
-  };
-
-  if (ctx.framework.dep === "expo") {
-    vars.INSTALL_CMD_EXTRA = `${pmInstallCommand(ctx.packageManager)} expo-secure-store`;
-  }
-
-  return vars;
-}
-
-function resolveTemplate(ctx: ProjectContext): TemplateName {
-  if (ctx.framework.dep === "next" && ctx.variant === "pages-router") {
-    return "nextjs-pages-router";
-  }
-  return FRAMEWORK_PROMPTS[ctx.framework.dep]?.template ?? "generic-fallback";
-}
-
-export const GENERIC_AGENT_PROMPT = loadTemplate("generic");
-
-export function buildAgentPrompt(ctx: ProjectContext): string {
-  return interpolate(loadTemplate(resolveTemplate(ctx)), buildVars(ctx));
-}
diff --git a/packages/cli-core/src/commands/init/prompts/md.d.ts b/packages/cli-core/src/commands/init/prompts/md.d.ts
deleted file mode 100644
index c94d67b1..00000000
--- a/packages/cli-core/src/commands/init/prompts/md.d.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-declare module "*.md" {
-  const content: string;
-  export default content;
-}
diff --git a/packages/cli-core/src/commands/init/prompts/nextjs-app-router.md b/packages/cli-core/src/commands/init/prompts/nextjs-app-router.md
deleted file mode 100644
index 29c90651..00000000
--- a/packages/cli-core/src/commands/init/prompts/nextjs-app-router.md
+++ /dev/null
@@ -1,129 +0,0 @@
-# Add Clerk to Next.js App Router
-
-Install `{{SDK}}`. Create `{{MIDDLEWARE_BASENAME}}.{{EXT}}` with `clerkMiddleware()` from `@clerk/nextjs/server` (in `{{BASE_DISPLAY}}`). Add `<ClerkProvider>` inside `<body>` in `{{LAYOUT_PATH}}`. Use `<Show>`, `<UserButton>`, `<SignInButton>`, `<SignUpButton>` from `@clerk/nextjs`.
-
-Latest docs: {{DOCS_URL}}
-
-## Keyless Mode
-
-No signup required. Without env vars (`{{ENV_VAR}}`, `CLERK_SECRET_KEY`), Clerk auto-generates temporary keys. A "Configure your application" prompt appears to claim later. Do NOT tell users to sign up, create accounts, get API keys, or add env vars before running.
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## {{BASE}}{{MIDDLEWARE_BASENAME}}.{{EXT}}
-
-```typescript
-import { clerkMiddleware } from "@clerk/nextjs/server";
-
-export default clerkMiddleware();
-
-export const config = {
-  matcher: [
-    "/((?!_next|[^?]*\\.(?:html?|css|js(?!on)|jpe?g|webp|png|gif|svg|ttf|woff2?|ico|csv|docx?|xlsx?|zip|webmanifest)).*)",
-    "/(api|trpc)(.*)",
-  ],
-};
-```
-
-## {{LAYOUT_PATH}}
-
-```typescript
-import { ClerkProvider, SignInButton, SignUpButton, Show, UserButton } from "@clerk/nextjs";
-
-export default function RootLayout({ children }: { children: React.ReactNode }) {
-  return (
-    <html lang="en">
-      <body>
-        <ClerkProvider>
-          <header>
-            <Show when="signed-out">
-              <SignInButton />
-              <SignUpButton />
-            </Show>
-            <Show when="signed-in">
-              <UserButton />
-            </Show>
-          </header>
-          {children}
-        </ClerkProvider>
-      </body>
-    </html>
-  );
-}
-```
-
-## {{BASE}}app/sign-in/[[...sign-in]]/page.{{JSX}}
-
-```typescript
-import { SignIn } from "@clerk/nextjs";
-export default function SignInPage() { return <SignIn />; }
-```
-
-## {{BASE}}app/sign-up/[[...sign-up]]/page.{{JSX}}
-
-```typescript
-import { SignUp } from "@clerk/nextjs";
-export default function SignUpPage() { return <SignUp />; }
-```
-
-## Environment
-
-Add to `.env.local`:
-
-```
-NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in
-NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up
-```
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `.env.local` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `clerkMiddleware()` from `@clerk/nextjs/server` in `{{MIDDLEWARE_BASENAME}}.{{EXT}}`
-- Add `<ClerkProvider>` inside `<body>` in `{{LAYOUT_PATH}}`
-- Import from `@clerk/nextjs` or `@clerk/nextjs/server`
-- Use App Router (`app/page.tsx`, `app/layout.tsx`)
-- Use `async/await` with `auth()` from `@clerk/nextjs/server`
-- Use existing package manager (`{{PM}}`)
-- Rely on keyless mode — skip account creation and API keys
-
-NEVER:
-
-- Reference `_app.tsx` or pages router
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Use old env var patterns
-- Import deprecated APIs (`withAuth`, old `currentUser`)
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Tell users to sign up or get API keys first
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { authMiddleware } from '@clerk/nextjs' // WRONG — use clerkMiddleware
-function MyApp({ Component, pageProps }) {}    // WRONG — pages router pattern
-pages/signin.js                                // WRONG — use app/ directory
-<SignedIn>                                     // WRONG — use <Show when="signed-in">
-<SignedOut>                                    // WRONG — use <Show when="signed-out">
-```
-
-## Verify Before Responding
-
-1. Is `clerkMiddleware()` used in `{{MIDDLEWARE_BASENAME}}.{{EXT}}`?
-2. Is `ClerkProvider` inside `<body>` in `{{LAYOUT_PATH}}`?
-3. Are imports only from `@clerk/nextjs` or `@clerk/nextjs/server`?
-4. Is it using App Router, not `_app.tsx` or `pages/`?
-5. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user in the nav. After signup succeeds and a profile icon appears, congratulate them. If a "Configure your application" callout appears, tell them to click it. Then recommend exploring: Organizations (https://clerk.com/docs/guides/organizations/overview), Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/nextjs-pages-router.md b/packages/cli-core/src/commands/init/prompts/nextjs-pages-router.md
deleted file mode 100644
index be2447a3..00000000
--- a/packages/cli-core/src/commands/init/prompts/nextjs-pages-router.md
+++ /dev/null
@@ -1,112 +0,0 @@
-# Add Clerk to Next.js Pages Router
-
-Install `{{SDK}}`. Create `{{MIDDLEWARE_BASENAME}}.{{EXT}}` with `clerkMiddleware()` from `@clerk/nextjs/server`. Wrap `<Component>` with `<ClerkProvider>` in `_app.{{JSX}}`. Use `<Show>`, `<UserButton>`, `<SignInButton>`, `<SignUpButton>` from `@clerk/nextjs`.
-
-Latest docs: {{DOCS_URL}}
-
-## Keyless Mode
-
-No signup required. Without env vars (`{{ENV_VAR}}`, `CLERK_SECRET_KEY`), Clerk auto-generates temporary keys. A "Configure your application" prompt appears to claim later. Do NOT tell users to sign up, create accounts, get API keys, or add env vars before running.
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## {{BASE}}{{MIDDLEWARE_BASENAME}}.{{EXT}}
-
-```typescript
-import { clerkMiddleware } from "@clerk/nextjs/server";
-
-export default clerkMiddleware();
-
-export const config = {
-  matcher: [
-    "/((?!_next|[^?]*\\.(?:html?|css|js(?!on)|jpe?g|webp|png|gif|svg|ttf|woff2?|ico|csv|docx?|xlsx?|zip|webmanifest)).*)",
-    "/(api|trpc)(.*)",
-  ],
-};
-```
-
-## {{BASE}}pages/\_app.{{JSX}}
-
-```typescript
-import { ClerkProvider } from "@clerk/nextjs";
-import type { AppProps } from "next/app";
-
-export default function MyApp({ Component, pageProps }: AppProps) {
-  return (
-    <ClerkProvider {...pageProps}>
-      <Component {...pageProps} />
-    </ClerkProvider>
-  );
-}
-```
-
-## {{BASE}}pages/sign-in/[[...sign-in]].{{JSX}}
-
-```typescript
-import { SignIn } from "@clerk/nextjs";
-export default function SignInPage() { return <SignIn />; }
-```
-
-## {{BASE}}pages/sign-up/[[...sign-up]].{{JSX}}
-
-```typescript
-import { SignUp } from "@clerk/nextjs";
-export default function SignUpPage() { return <SignUp />; }
-```
-
-## Environment
-
-Add to `.env.local`:
-
-```
-NEXT_PUBLIC_CLERK_SIGN_IN_URL=/sign-in
-NEXT_PUBLIC_CLERK_SIGN_UP_URL=/sign-up
-```
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `.env.local` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `clerkMiddleware()` from `@clerk/nextjs/server` in `{{MIDDLEWARE_BASENAME}}.{{EXT}}`
-- Wrap `<Component>` with `<ClerkProvider {...pageProps}>` in `_app.{{JSX}}`
-- Import from `@clerk/nextjs` or `@clerk/nextjs/server`
-- Use `async/await` with `auth()` from `@clerk/nextjs/server` in API routes
-- Use existing package manager (`{{PM}}`)
-- Rely on keyless mode — skip account creation and API keys
-
-NEVER:
-
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Use old env var patterns
-- Import deprecated APIs (`withAuth`, old `currentUser`)
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Tell users to sign up or get API keys first
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { authMiddleware } from '@clerk/nextjs' // WRONG — use clerkMiddleware
-<SignedIn>                                     // WRONG — use <Show when="signed-in">
-<SignedOut>                                    // WRONG — use <Show when="signed-out">
-```
-
-## Verify Before Responding
-
-1. Is `clerkMiddleware()` used in `{{MIDDLEWARE_BASENAME}}.{{EXT}}`?
-2. Is `<ClerkProvider {...pageProps}>` wrapping `<Component>` in `_app.{{JSX}}`?
-3. Are imports only from `@clerk/nextjs` or `@clerk/nextjs/server`?
-4. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user in the nav. After signup succeeds and a profile icon appears, congratulate them. If a "Configure your application" callout appears, tell them to click it. Then recommend exploring: Organizations (https://clerk.com/docs/guides/organizations/overview), Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/nuxt.md b/packages/cli-core/src/commands/init/prompts/nuxt.md
deleted file mode 100644
index 7fa00a3a..00000000
--- a/packages/cli-core/src/commands/init/prompts/nuxt.md
+++ /dev/null
@@ -1,94 +0,0 @@
-# Add Clerk to Nuxt
-
-Install `{{SDK}}`. Add `@clerk/nuxt` to the `modules` array in `nuxt.config.ts`. Middleware is auto-configured. Use `<Show>`, `<SignIn>`, `<SignUp>`, `<UserButton>` (auto-imported).
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## nuxt.config.ts
-
-```typescript
-export default defineNuxtConfig({
-  modules: ["@clerk/nuxt"],
-});
-```
-
-## pages/sign-in/[...slug].vue
-
-```vue
-<template>
-  <SignIn />
-</template>
-```
-
-## pages/sign-up/[...slug].vue
-
-```vue
-<template>
-  <SignUp />
-</template>
-```
-
-## Example usage in a component
-
-```vue
-<template>
-  <header>
-    <Show when="signed-out">
-      <SignInButton />
-      <SignUpButton />
-    </Show>
-    <Show when="signed-in">
-      <UserButton />
-    </Show>
-  </header>
-</template>
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `NUXT_CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Add `'@clerk/nuxt'` to the `modules` array in `nuxt.config.ts`
-- Let Nuxt auto-import Clerk components (no manual imports needed)
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Manually configure middleware (Nuxt module handles it)
-- Manually import Clerk components in `.vue` files (auto-imported)
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Import from `@clerk/vue` — use `@clerk/nuxt`
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { clerkMiddleware } from '@clerk/nuxt' // WRONG — module auto-configures middleware
-<SignedIn>                                    // WRONG — use <Show when="signed-in">
-<SignedOut>                                   // WRONG — use <Show when="signed-out">
-import { SignIn } from "@clerk/vue"           // WRONG — auto-imported by Nuxt module
-```
-
-## Verify Before Responding
-
-1. Is `'@clerk/nuxt'` in the `modules` array in `nuxt.config.ts`?
-2. Are Clerk components used without manual imports?
-3. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/react-router.md b/packages/cli-core/src/commands/init/prompts/react-router.md
deleted file mode 100644
index 70a4dbc0..00000000
--- a/packages/cli-core/src/commands/init/prompts/react-router.md
+++ /dev/null
@@ -1,115 +0,0 @@
-# Add Clerk to React Router
-
-Install `{{SDK}}`. Enable middleware in `react-router.config.ts`. Set up `clerkMiddleware()` and `ClerkProvider` in `app/root.tsx`. Use `<Show>`, `<UserButton>`, `<SignInButton>`, `<SignUpButton>` from `@clerk/react-router`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## react-router.config.ts
-
-```typescript
-import type { Config } from "@react-router/dev/config";
-
-export default {
-  future: {
-    v8_middleware: true,
-  },
-} satisfies Config;
-```
-
-## app/root.tsx
-
-```typescript
-import { clerkMiddleware, rootAuthLoader } from "@clerk/react-router/server";
-import { ClerkProvider } from "@clerk/react-router";
-import type { Route } from "./+types/root";
-
-export const middleware: Route.MiddlewareFunction[] = [clerkMiddleware()];
-
-export const loader = (args: Route.LoaderArgs) => rootAuthLoader(args);
-
-export default function Root({ loaderData }: Route.ComponentProps) {
-  return (
-    <ClerkProvider loaderData={loaderData}>
-      {/* your app content */}
-    </ClerkProvider>
-  );
-}
-```
-
-## app/routes/sign-in.{{JSX}}
-
-```typescript
-import { SignIn } from "@clerk/react-router";
-export default function SignInPage() { return <SignIn />; }
-```
-
-## app/routes/sign-up.{{JSX}}
-
-```typescript
-import { SignUp } from "@clerk/react-router";
-export default function SignUpPage() { return <SignUp />; }
-```
-
-## app/routes.ts
-
-```typescript
-import { type RouteConfig, route } from "@react-router/dev/routes";
-
-export default [
-  route("sign-in/*", "routes/sign-in.tsx"),
-  route("sign-up/*", "routes/sign-up.tsx"),
-] satisfies RouteConfig;
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Enable `future: { v8_middleware: true }` in `react-router.config.ts`
-- Use `clerkMiddleware()` from `@clerk/react-router/server` in `app/root.tsx`
-- Use `rootAuthLoader` for the root loader
-- Wrap content with `<ClerkProvider loaderData={loaderData}>`
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Skip the `rootAuthLoader` in the root route
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Import from `@clerk/nextjs` or `@clerk/react` — use `@clerk/react-router`
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { authMiddleware } from '@clerk/react-router' // WRONG — use clerkMiddleware
-<SignedIn>                                           // WRONG — use <Show when="signed-in">
-<SignedOut>                                          // WRONG — use <Show when="signed-out">
-import { ClerkProvider } from "@clerk/react"         // WRONG — use @clerk/react-router
-```
-
-## Verify Before Responding
-
-1. Is `v8_middleware: true` set in `react-router.config.ts`?
-2. Is `clerkMiddleware()` exported in `app/root.tsx`?
-3. Is `rootAuthLoader` used as the root loader?
-4. Is `<ClerkProvider loaderData={loaderData}>` wrapping the app?
-5. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/react.md b/packages/cli-core/src/commands/init/prompts/react.md
deleted file mode 100644
index 67a86c93..00000000
--- a/packages/cli-core/src/commands/init/prompts/react.md
+++ /dev/null
@@ -1,94 +0,0 @@
-# Add Clerk to React
-
-Install `{{SDK}}`. Wrap the app in `<ClerkProvider>` in `{{BASE}}main.{{JSX}}`. Use `<Show>`, `<SignInButton>`, `<SignUpButton>`, `<UserButton>` from `@clerk/react`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## {{BASE}}main.{{JSX}}
-
-```typescript
-import { StrictMode } from "react";
-import { createRoot } from "react-dom/client";
-import App from "./App.{{JSX}}";
-import { ClerkProvider } from "@clerk/react";
-
-createRoot(document.getElementById("root")!).render(
-  <StrictMode>
-    <ClerkProvider afterSignOutUrl="/">
-      <App />
-    </ClerkProvider>
-  </StrictMode>
-);
-```
-
-## App.{{JSX}}
-
-```typescript
-import { Show, SignInButton, SignUpButton, UserButton } from "@clerk/react";
-
-export default function App() {
-  return (
-    <header>
-      <Show when="signed-out">
-        <SignInButton />
-        <SignUpButton />
-      </Show>
-      <Show when="signed-in">
-        <UserButton />
-      </Show>
-    </header>
-  );
-}
-```
-
-## Environment
-
-Env var (`{{ENV_VAR}}`) is in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `@clerk/react` (not any other Clerk package)
-- Reference env var as `{{ENV_VAR}}` in `{{ENV_FILE}}`
-- Wrap the entire app in `<ClerkProvider>` within `{{BASE}}main.{{JSX}}`
-- Use `<Show>`, `<SignInButton>`, `<SignUpButton>`, `<UserButton>`
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `frontendApi` in place of `publishableKey`
-- Use older env var names like `REACT_APP_CLERK_FRONTEND_API` or `VITE_REACT_APP_CLERK_PUBLISHABLE_KEY`
-- Manually pass `publishableKey` as a prop to `<ClerkProvider>`
-- Place `<ClerkProvider>` deeper in the component tree instead of `{{BASE}}main.{{JSX}}`
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { SignedIn, SignedOut } from "@clerk/react" // WRONG — use <Show>
-<ClerkProvider publishableKey={key}>              // WRONG — reads from env automatically
-frontendApi="..."                                 // WRONG — removed, use publishableKey env var
-REACT_APP_CLERK_FRONTEND_API                      // WRONG — use {{ENV_VAR}}
-```
-
-## Verify Before Responding
-
-1. Is `<ClerkProvider>` in `{{BASE}}main.{{JSX}}` without a manual `publishableKey` prop?
-2. Is env var named `{{ENV_VAR}}`?
-3. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-4. No usage of `frontendApi`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/tanstack-start.md b/packages/cli-core/src/commands/init/prompts/tanstack-start.md
deleted file mode 100644
index a6478fc4..00000000
--- a/packages/cli-core/src/commands/init/prompts/tanstack-start.md
+++ /dev/null
@@ -1,108 +0,0 @@
-# Add Clerk to TanStack Start
-
-Install `{{SDK}}`. Add `clerkMiddleware()` to `src/start.ts`. Wrap content with `<ClerkProvider>` in `src/routes/__root.tsx`. Use `<Show>`, `<UserButton>`, `<SignInButton>`, `<SignUpButton>` from `@clerk/tanstack-react-start`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## src/start.ts
-
-```typescript
-import { createStart } from "@tanstack/react-start/server";
-import { clerkMiddleware } from "@clerk/tanstack-react-start/server";
-
-export default createStart({
-  requestMiddleware: [clerkMiddleware()],
-});
-```
-
-## src/routes/\_\_root.tsx
-
-```typescript
-import { ClerkProvider } from "@clerk/tanstack-react-start";
-import { createRootRoute, Outlet } from "@tanstack/react-router";
-
-export const Route = createRootRoute({
-  component: RootLayout,
-});
-
-function RootLayout() {
-  return (
-    <ClerkProvider>
-      <Outlet />
-    </ClerkProvider>
-  );
-}
-```
-
-## src/routes/sign-in.$.{{JSX}}
-
-```typescript
-import { createFileRoute } from "@tanstack/react-router";
-import { SignIn } from "@clerk/tanstack-react-start";
-
-export const Route = createFileRoute("/sign-in/$")({
-  component: () => <SignIn />,
-});
-```
-
-## src/routes/sign-up.$.{{JSX}}
-
-```typescript
-import { createFileRoute } from "@tanstack/react-router";
-import { SignUp } from "@clerk/tanstack-react-start";
-
-export const Route = createFileRoute("/sign-up/$")({
-  component: () => <SignUp />,
-});
-```
-
-## Environment
-
-Env vars (`{{ENV_VAR}}` and `CLERK_SECRET_KEY`) are in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `clerkMiddleware()` from `@clerk/tanstack-react-start/server` in `src/start.ts`
-- Wrap content with `<ClerkProvider>` in `src/routes/__root.tsx`
-- Use `createFileRoute` for sign-in/sign-up routes with `$` splat
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use `authMiddleware()` (replaced by `clerkMiddleware()`)
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Import from `@clerk/react` or `@clerk/nextjs` — use `@clerk/tanstack-react-start`
-- Skip `requestMiddleware` in `createStart` config
-
-## Deprecated (DO NOT use)
-
-```typescript
-import { authMiddleware } from '@clerk/tanstack-react-start' // WRONG — use clerkMiddleware
-<SignedIn>                                                   // WRONG — use <Show when="signed-in">
-<SignedOut>                                                  // WRONG — use <Show when="signed-out">
-import { ClerkProvider } from "@clerk/react"                 // WRONG — use @clerk/tanstack-react-start
-```
-
-## Verify Before Responding
-
-1. Is `clerkMiddleware()` in `requestMiddleware` in `src/start.ts`?
-2. Is `<ClerkProvider>` wrapping `<Outlet />` in `src/routes/__root.tsx`?
-3. Are sign-in/sign-up routes using `createFileRoute` with `$` splat?
-4. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/prompts/vue.md b/packages/cli-core/src/commands/init/prompts/vue.md
deleted file mode 100644
index 80bb8a92..00000000
--- a/packages/cli-core/src/commands/init/prompts/vue.md
+++ /dev/null
@@ -1,85 +0,0 @@
-# Add Clerk to Vue
-
-Install `{{SDK}}`. Add `clerkPlugin` to the Vue app in `{{BASE}}main.ts`. Use `<Show>`, `<SignInButton>`, `<SignUpButton>`, `<UserButton>` from `@clerk/vue`.
-
-Latest docs: {{DOCS_URL}}
-
-## Install
-
-```bash
-{{INSTALL_CMD}}
-```
-
-## {{BASE}}main.ts
-
-```typescript
-import { createApp } from 'vue';
-import App from './App.vue';
-import { clerkPlugin } from '@clerk/vue';
-
-const app = createApp(App);
-app.use(clerkPlugin, {
-  publishableKey: import.meta.env.{{ENV_VAR}},
-});
-app.mount('#app');
-```
-
-## Example usage in App.vue
-
-```vue
-<script setup>
-import { Show, SignInButton, SignUpButton, UserButton } from "@clerk/vue";
-</script>
-
-<template>
-  <header>
-    <Show when="signed-out">
-      <SignInButton />
-      <SignUpButton />
-    </Show>
-    <Show when="signed-in">
-      <UserButton />
-    </Show>
-  </header>
-</template>
-```
-
-## Environment
-
-Env var (`{{ENV_VAR}}`) is in `{{ENV_FILE}}` via `clerk env pull`.
-
-## Rules
-
-ALWAYS:
-
-- Use `clerkPlugin` from `@clerk/vue` in `{{BASE}}main.ts`
-- Pass `publishableKey: import.meta.env.{{ENV_VAR}}` to `clerkPlugin`
-- Use `<Show>` for conditional rendering
-- Use existing package manager (`{{PM}}`)
-
-NEVER:
-
-- Use deprecated `<SignedIn>`, `<SignedOut>` (replaced by `<Show>`)
-- Import from `@clerk/react` or `@clerk/nextjs` — use `@clerk/vue`
-- Use old env var names
-
-## Deprecated (DO NOT use)
-
-```typescript
-<SignedIn>   // WRONG — use <Show when="signed-in">
-<SignedOut>  // WRONG — use <Show when="signed-out">
-```
-
-## Verify Before Responding
-
-1. Is `clerkPlugin` used with `app.use()` in `{{BASE}}main.ts`?
-2. Is `publishableKey` reading from `import.meta.env.{{ENV_VAR}}`?
-3. Is it using `<Show>` instead of `<SignedIn>`/`<SignedOut>`?
-
-If any fails, revise.
-
-## After Setup
-
-Have the user sign up as their first test user. After signup succeeds and a profile icon appears, congratulate them. Then recommend exploring: Components (https://clerk.com/docs/reference/components/overview), Dashboard (https://dashboard.clerk.com/).
-
-If you (the agent) need to create test users programmatically to exercise auth-gated code, use a `+clerk_test` email suffix. Clerk accepts `424242` as the OTP for these addresses, so you don't need inbox access. Development instances only.
diff --git a/packages/cli-core/src/commands/init/scaffold.ts b/packages/cli-core/src/commands/init/scaffold.ts
index ef50b862..2eafa6ed 100644
--- a/packages/cli-core/src/commands/init/scaffold.ts
+++ b/packages/cli-core/src/commands/init/scaffold.ts
@@ -25,7 +25,7 @@ const SCAFFOLDERS = [
 /**
  * Run the matching scaffolder's enrichContext to populate framework-specific
  * fields (variant, layoutPath, middlewareBasename) on the context.
- * Must be called before scaffold() or buildAgentPrompt().
+ * Must be called before scaffold().
  */
 export async function enrichProjectContext(ctx: ProjectContext): Promise<void> {
   const scaffolder = SCAFFOLDERS.find((s) => s.dep === ctx.framework.dep);
diff --git a/packages/cli-core/src/globals.d.ts b/packages/cli-core/src/globals.d.ts
index ed01cbdb..0d3ac77d 100644
--- a/packages/cli-core/src/globals.d.ts
+++ b/packages/cli-core/src/globals.d.ts
@@ -1,3 +1,8 @@
+declare module "*.md" {
+  const content: string;
+  export default content;
+}
+
 declare const CLI_VERSION: string | undefined;
 
 declare const CLI_ENV_PROFILES:
diff --git a/packages/cli-core/src/lib/installer.ts b/packages/cli-core/src/lib/installer.ts
index ae59eb30..3e04b960 100644
--- a/packages/cli-core/src/lib/installer.ts
+++ b/packages/cli-core/src/lib/installer.ts
@@ -12,6 +12,7 @@ import { access, realpath, stat } from "node:fs/promises";
 import { homedir } from "node:os";
 import { delimiter, join, sep } from "node:path";
 import { UPDATE_PACKAGE_NAME } from "./constants.ts";
+import { pmInstallCommand, type PackageManager } from "./package-manager.ts";
 
 // ── Types ────────────────────────────────────────────────────────────────────
 
@@ -354,16 +355,10 @@ function normalizeWindowsPath(p: string): string {
 
 /** Human-readable install/update command for the given installer. */
 export function globalInstallCommand(installer: Installer, packageSpec: string): string {
-  switch (installer) {
-    case "bun":
-      return `bun add -g ${packageSpec}`;
-    case "pnpm":
-      return `pnpm add -g ${packageSpec}`;
-    case "yarn":
-      return `yarn global add ${packageSpec}`;
-    case "homebrew":
-      return `brew upgrade ${UPDATE_PACKAGE_NAME}`;
-    default:
-      return `npm install -g ${packageSpec}`;
-  }
+  if (installer === "homebrew") return `brew upgrade ${UPDATE_PACKAGE_NAME}`;
+  if (installer === "yarn") return `yarn global add ${packageSpec}`;
+
+  // For bun, pnpm, and npm the global form is the local `<pm> add` command
+  // with a `-g` flag appended — reuse `pmInstallCommand` as the base.
+  return `${pmInstallCommand(installer as PackageManager)} -g ${packageSpec}`;
 }
diff --git a/packages/cli-core/src/lib/package-manager.ts b/packages/cli-core/src/lib/package-manager.ts
index 06c67266..34fb6c18 100644
--- a/packages/cli-core/src/lib/package-manager.ts
+++ b/packages/cli-core/src/lib/package-manager.ts
@@ -8,6 +8,18 @@ export const PACKAGE_MANAGERS = ["bun", "pnpm", "yarn", "npm"] as const;
 
 export type PackageManager = (typeof PACKAGE_MANAGERS)[number];
 
+const PM_INSTALL_COMMANDS = {
+  bun: "bun add",
+  yarn: "yarn add",
+  pnpm: "pnpm add",
+  npm: "npm install",
+} satisfies Record<PackageManager, string>;
+
+/** Returns the `<pm> add`-style command for installing dependencies. */
+export function pmInstallCommand(pm: PackageManager): string {
+  return PM_INSTALL_COMMANDS[pm];
+}
+
 /** Detects the package manager in use by checking for lockfiles in `cwd`. */
 export async function detectPackageManager(cwd: string): Promise<PackageManager> {
   const checks: Array<{ files: string[]; pm: PackageManager }> = [
diff --git a/packages/cli-core/src/test/integration/agent-mode.test.ts b/packages/cli-core/src/test/integration/agent-mode.test.ts
index bf7b4b60..327a5877 100644
--- a/packages/cli-core/src/test/integration/agent-mode.test.ts
+++ b/packages/cli-core/src/test/integration/agent-mode.test.ts
@@ -8,12 +8,6 @@ import { useIntegrationTestHarness, http, clerk, readConfig, MOCK_APP } from "./
 
 useIntegrationTestHarness();
 
-test("init --prompt outputs structured agent prompt without API calls", async () => {
-  const { stdout } = await clerk("init", "--prompt");
-  expect(stdout).toContain("clerk init -y");
-  expect(http.requests.length).toBe(0);
-});
-
 test("link with --app writes the profile in agent mode", async () => {
   http.mock({
     [`/applications/${MOCK_APP.application_id}`]: MOCK_APP,
diff --git a/packages/cli-core/src/test/integration/init-options.test.ts b/packages/cli-core/src/test/integration/init-options.test.ts
index a67f063b..5e9bc1d3 100644
--- a/packages/cli-core/src/test/integration/init-options.test.ts
+++ b/packages/cli-core/src/test/integration/init-options.test.ts
@@ -10,11 +10,10 @@ import { useIntegrationTestHarness, clerk } from "./lib/harness.ts";
 useIntegrationTestHarness();
 
 test("init accepts --app without rejecting it as an unknown option", async () => {
-  // --prompt exits before any auth/link/scaffold side effects. If --app is
-  // not registered with Commander, parseAsync throws `commander.unknownOption`
-  // before --prompt can short-circuit, and `clerk` (strict) throws.
-  const { stdout, stderr, exitCode } = await clerk("init", "--app", "app_123", "--prompt");
-  expect(exitCode).toBe(0);
-  expect(stderr).not.toContain("unknown option");
-  expect(stdout).toContain("clerk init -y");
+  // If --app is not registered with Commander, parseAsync throws
+  // `commander.unknownOption` which surfaces as "unknown option" in stderr.
+  // Init exits non-zero in this test cwd (no framework detected) — that's
+  // expected; we only care that the option pipeline accepted --app.
+  const result = await clerk.raw("init", "--app", "app_123");
+  expect(result.stderr).not.toContain("unknown option");
 });
diff --git a/packages/cli-core/src/test/integration/input-json.test.ts b/packages/cli-core/src/test/integration/input-json.test.ts
index 93e6a3eb..0c23560b 100644
--- a/packages/cli-core/src/test/integration/input-json.test.ts
+++ b/packages/cli-core/src/test/integration/input-json.test.ts
@@ -27,23 +27,21 @@ beforeEach(async () => {
 });
 
 test("init --input-json passes options through Commander pipeline", async () => {
-  // {"prompt":true} expands to --prompt, short-circuiting init to log the agent handoff
-  const { stdout } = await clerk("init", "--input-json", '{"prompt":true}');
-  expect(stdout).toContain("clerk init -y");
+  // {"yes":true} expands to --yes; init still fails (no framework in test cwd) but
+  // the "unknown option" path would surface a different stderr if Commander rejected
+  // the expanded flag, so this proves expansion + acceptance.
+  const result = await clerk.raw("init", "--input-json", '{"yes":true}');
+  expect(result.stderr).not.toContain("unknown option");
 });
 
 test("explicit CLI flags override --input-json values", async () => {
-  // --input-json sets mode=human, but --mode agent after it overrides. --prompt on the
-  // subcommand short-circuits so we don't trigger bootstrap.
-  const { stdout } = await clerk(
-    "init",
-    "--prompt",
-    "--input-json",
-    '{"mode":"human"}',
-    "--mode",
-    "agent",
-  );
-  expect(stdout).toContain("clerk init -y");
+  // --input-json sets mode=human, but --mode agent later overrides. The post-parse
+  // mode is observable via the structured-JSON error format that agent mode emits.
+  const result = await clerk.raw("init", "--input-json", '{"mode":"human"}', "--mode", "agent");
+  expect(result.exitCode).not.toBe(0);
+  // Agent mode emits structured JSON to stderr; human mode emits plain text.
+  const parsed = JSON.parse(result.stderr);
+  expect(parsed.error).toBeDefined();
 });
 
 test("doctor --input-json with json:true outputs JSON", async () => {
@@ -103,8 +101,11 @@ test("rejects unknown options via Commander", async () => {
 });
 
 test("empty JSON object is a no-op", async () => {
-  const { stdout } = await clerk("init", "--prompt", "--input-json", "{}");
-  expect(stdout).toContain("clerk init -y");
+  // Empty JSON adds no flags. doctor is non-side-effecting and returns JSON
+  // when --json is in argv elsewhere — here we just need a clean exit.
+  const result = await clerk.raw("doctor", "--input-json", "{}", "--json");
+  const parsed = JSON.parse(result.stdout);
+  expect(Array.isArray(parsed)).toBe(true);
 });
 
 test("@file.json reads options from a temp file", async () => {
@@ -219,21 +220,22 @@ test("--input-json after nested subcommand targets that subcommand", async () =>
 });
 
 test("noSkills negated boolean via --input-json", async () => {
-  // noSkills:true → --no-skills. Commander must accept the negated flag without error.
-  const { stdout } = await clerk(
-    "init",
-    "--prompt",
-    "--input-json",
-    '{"prompt":true,"noSkills":true}',
-  );
-  expect(stdout).toContain("clerk init -y");
+  // noSkills:true → --no-skills. Init will exit non-zero (no framework in test cwd)
+  // but Commander would surface "unknown option" before the action runs if the
+  // negated flag wasn't accepted.
+  const result = await clerk.raw("init", "--input-json", '{"yes":true,"noSkills":true}');
+  expect(result.stderr).not.toContain("unknown option");
 });
 
 test("--input-json is registered as a global option", async () => {
   // --input-json before the subcommand expands to flags at the root-program level.
   // --mode is a root-level flag, so this works; subcommand-specific flags would not.
-  const { stdout } = await clerk("--input-json", '{"mode":"agent"}', "init", "--prompt");
-  expect(stdout).toContain("clerk init -y");
+  // doctor exits non-zero in this harness; the structured-JSON error format on
+  // stderr is the agent-mode signature, which proves --mode agent was applied.
+  const result = await clerk.raw("--input-json", '{"mode":"agent"}', "doctor", "--json");
+  expect(result.exitCode).not.toBe(0);
+  const parsed = JSON.parse(result.stderr);
+  expect(parsed.error).toBeDefined();
 });
 
 test("structured JSON error in agent mode for invalid JSON", async () => {