feat(init): Allow agent init without implicit app selection

.changeset/agent-init-keyless.md

@@ -0,0 +1,5 @@
+---
+"clerk": patch
+---
+
+Allow `clerk init` to run in agent mode without requiring `--app`. For keyless-capable frameworks, agent init now uses keyless setup when no real Clerk app target is provided; explicit `--app` or an existing linked profile still uses the authenticated app-linking flow, including the normal login fallback when needed. Agent init no longer creates, auto-selects, or auto-links a Clerk application when no app target is provided.

packages/cli-core/src/commands/init/README.md

@@ -1,6 +1,6 @@
 # Init Command
 
-Initializes Clerk in a project by authenticating the user, linking a Clerk application, installing the SDK, pulling environment variables, and scaffolding framework-specific boilerplate.
+Initializes Clerk in a project by detecting the framework, installing the SDK, and scaffolding framework-specific boilerplate. Depending on mode and framework support, init either uses keyless development keys or links to a real Clerk application and pulls environment variables.
 
 ## Usage
 
@@ -36,15 +36,18 @@ When running in agent mode (`--mode agent` or non-TTY), the command runs the ful
 - For **existing projects**: framework and package manager are auto-detected, no flags required
 - 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
+- For keyless-capable frameworks with no `--app` and no linked profile, init uses keyless and does not require auth
+- For frameworks that require API keys, init will not pick or create an app in agent mode; pass `--app <id>` or link the project first to pull real keys
 
 ## Flow
 
 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
+2. Determines auth mode:
+   - **Real app target** (`--app` or linked profile): authenticates, links if needed, and pulls real API keys into `.env`
+   - **Agent + keyless-capable framework + no real app target**: uses keyless mode — the app runs on auto-generated dev keys and the user can connect a Clerk account later with `clerk auth login`
+   - **Agent + non-keyless framework + no real app target**: scaffolds locally and prints manual setup instructions instead of selecting or creating an app
+   - **Human mode + bootstrap + keyless-capable framework + not authenticated**: uses keyless mode
+   - **Human mode + existing project + not authenticated**: runs the authenticated flow, which triggers an interactive login so real keys can be pulled
 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
@@ -78,7 +81,7 @@ Detects the project's framework from `package.json` dependencies (checked top-to
 | `express`               | Express        | `@clerk/express`              | `CLERK_PUBLISHABLE_KEY`             | No      |
 | `fastify`               | Fastify        | `@clerk/fastify`              | `CLERK_PUBLISHABLE_KEY`             | No      |
 
-The **Keyless** column indicates whether the framework's Clerk SDK supports keyless mode (auto-generated temporary dev keys). Keyless auto-selection only applies during bootstrap (new projects) — re-running `clerk init` in an existing project always uses the authenticated flow (prompting login when signed out) so real keys can be pulled via `clerk env pull`. During bootstrap of a non-keyless framework with `--yes` and no credentials, `clerk init` skips authentication and prints manual setup instructions instead of blocking on a login prompt.
+The **Keyless** column indicates whether the framework's Clerk SDK supports keyless mode (auto-generated temporary dev keys). In human mode, keyless auto-selection only applies during bootstrap (new projects). In agent mode, keyless-capable frameworks use keyless whenever no real app target is provided by `--app` or a linked profile. For non-keyless frameworks without a real app target, agent mode prints manual setup instructions instead of selecting or creating an app.
 
 Package manager is detected from lock files: `bun.lockb`/`bun.lock` → bun, `yarn.lock` → yarn, `pnpm-lock.yaml` → pnpm, else npm.
 
@@ -223,15 +226,15 @@ Implementation lives in [`skills.ts`](./skills.ts). Note that the E2E fixture se
 
 ## API Endpoints
 
-| Step                   | Method | Base URL                        | Endpoint                       | Description                                                                                                                                         |
-| ---------------------- | ------ | ------------------------------- | ------------------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Create accountless app | `POST` | `CLERK_BAPI_URL` (default BAPI) | `/v1/accountless_applications` | Creates a temporary keyless Clerk application; returns `publishable_key`, `secret_key`, and `claim_url`. Only called in the keyless bootstrap path. |
+| Step                   | Method | Base URL                        | Endpoint                       | Description                                                                                                                           |
+| ---------------------- | ------ | ------------------------------- | ------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------- |
+| Create accountless app | `POST` | `CLERK_BAPI_URL` (default BAPI) | `/v1/accountless_applications` | Creates a temporary keyless Clerk application; returns `publishable_key`, `secret_key`, and `claim_url`. Only called in keyless mode. |
 
 See [auth/README.md](../auth/README.md), [link/README.md](../link/README.md), and [env/README.md](../env/README.md) for the API endpoints used by each step.
 
 ## Keyless breadcrumb
 
-In the keyless bootstrap path, after calling `POST /v1/accountless_applications`, `clerk init` writes `.clerk/keyless.json` to the project root. This file records the claim token extracted from `claim_url` so that `clerk auth login` can automatically claim the temporary application the next time the user authenticates.
+In keyless mode, after calling `POST /v1/accountless_applications`, `clerk init` writes `.clerk/keyless.json` to the project root. This file records the claim token extracted from `claim_url` so that `clerk auth login` can automatically claim the temporary application the next time the user authenticates.
 
 ```json
 {

packages/cli-core/src/commands/init/index.test.ts

@@ -341,6 +341,119 @@ describe("init", () => {
     expect(linkMod.link).not.toHaveBeenCalled();
   });
 
+  test("agent mode with keyless framework uses keyless without an app target", async () => {
+    setup({ isAgent: true, email: "user@example.com" });
+
+    const keylessCtx = {
+      ...FAKE_CTX,
+      existingClerk: false,
+      framework: { ...FAKE_CTX.framework, supportsKeyless: true },
+    };
+    spyOn(context, "gatherContext").mockResolvedValue(keylessCtx);
+    spyOn(scaffoldMod, "scaffold").mockResolvedValue({
+      actions: [{ type: "create", path: "middleware.ts", content: "", description: "" }],
+      postInstructions: [],
+    });
+
+    await init({});
+
+    expect(heuristics.printKeylessInfo).toHaveBeenCalled();
+    expect(linkMod.link).not.toHaveBeenCalled();
+    expect(pullMod.pull).not.toHaveBeenCalled();
+  });
+
+  test("agent mode with keyless framework uses linked profile as a real app target", async () => {
+    setup({ isAgent: true, email: "user@example.com" });
+
+    const keylessCtx = {
+      ...FAKE_CTX,
+      existingClerk: false,
+      framework: { ...FAKE_CTX.framework, supportsKeyless: true },
+    };
+    spyOn(context, "gatherContext").mockResolvedValue(keylessCtx);
+    spyOn(config, "resolveProfile").mockResolvedValue({
+      profile: { appId: "app_123" },
+    } as never);
+    spyOn(scaffoldMod, "scaffold").mockResolvedValue({
+      actions: [{ type: "create", path: "middleware.ts", content: "", description: "" }],
+      postInstructions: [],
+    });
+
+    await init({});
+
+    expect(heuristics.printKeylessInfo).not.toHaveBeenCalled();
+    expect(linkMod.link).not.toHaveBeenCalled();
+    expect(pullMod.pull).toHaveBeenCalledWith({ file: ".env", cwd: keylessCtx.cwd });
+  });
+
+  test("agent mode with keyless framework and --app uses real app flow", async () => {
+    setup({ isAgent: true, email: "user@example.com" });
+
+    const keylessCtx = {
+      ...FAKE_CTX,
+      existingClerk: false,
+      framework: { ...FAKE_CTX.framework, supportsKeyless: true },
+    };
+    spyOn(context, "gatherContext").mockResolvedValue(keylessCtx);
+    spyOn(scaffoldMod, "scaffold").mockResolvedValue({
+      actions: [{ type: "create", path: "middleware.ts", content: "", description: "" }],
+      postInstructions: [],
+    });
+
+    await init({ app: "app_abc" });
+
+    expect(heuristics.printKeylessInfo).not.toHaveBeenCalled();
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: "app_abc",
+      cwd: keylessCtx.cwd,
+    });
+    expect(pullMod.pull).toHaveBeenCalledWith({ file: ".env", cwd: keylessCtx.cwd });
+  });
+
+  test("agent mode with non-keyless framework and no app target prints manual setup", async () => {
+    const { captured } = setup({ isAgent: true, email: "user@example.com" });
+
+    const noKeylessCtx = {
+      ...FAKE_CTX,
+      existingClerk: false,
+      framework: {
+        dep: "vue",
+        name: "Vue",
+        sdk: "@clerk/vue",
+        envVar: "VITE_CLERK_PUBLISHABLE_KEY",
+        envFile: ".env.local" as const,
+      },
+      envFile: ".env.local",
+    };
+    spyOn(context, "gatherContext").mockResolvedValue(noKeylessCtx);
+    spyOn(scaffoldMod, "scaffold").mockResolvedValue({
+      actions: [{ type: "create", path: "src/main.ts", content: "", description: "" }],
+      postInstructions: [],
+    });
+
+    await captured.run(() => init({}));
+
+    expect(linkMod.link).not.toHaveBeenCalled();
+    expect(pullMod.pull).not.toHaveBeenCalled();
+    expect(loginMod.login).not.toHaveBeenCalled();
+    expect(captured.err).toContain("clerk init --app <app_id>");
+  });
+
+  test("agent mode with real app target and no auth launches login", async () => {
+    setup({ isAgent: true });
+    spyOn(context, "gatherContext").mockResolvedValue(FAKE_CTX);
+
+    await init({ app: "app_abc" });
+
+    expect(loginMod.login).toHaveBeenCalledWith({ showNextSteps: false });
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: "app_abc",
+      cwd: FAKE_CTX.cwd,
+    });
+  });
+
   test("-y flag skips auth prompt and defaults to unauthenticated mode", async () => {
     setup();
     setupBootstrapSuccess();

packages/cli-core/src/commands/init/index.ts

@@ -56,14 +56,15 @@ type InitOptions = {
 
 export async function init(options: InitOptions = {}) {
   const cwd = process.cwd();
+  const agent = isAgent();
 
   const frameworkOverride = options.framework
     ? (lookupFramework(options.framework) ?? undefined)
     : undefined;
 
   // In agent mode, implicitly enable --yes to skip all confirmation prompts.
   const overrides: BootstrapOverrides = {
-    skipConfirm: options.yes || isAgent(),
+    skipConfirm: options.yes || agent,
     pmOverride: options.pm,
     nameOverride: options.name,
   };
@@ -85,12 +86,21 @@ export async function init(options: InitOptions = {}) {
   await enrichProjectContext(ctx);
 
   const authed = await isAuthenticated();
-  const keyless = resolveKeylessMode(bootstrap, ctx, authed);
+  const linkedProfile = agent && !options.app ? await resolveProfile(ctx.cwd) : undefined;
+  const hasRealAppTarget = Boolean(options.app || linkedProfile);
+  const keyless = resolveKeylessMode({
+    agent,
+    bootstrap,
+    ctx,
+    authed,
+    hasRealAppTarget,
+  });
   ctx.keyless = keyless;
 
-  const skipAuth = !keyless && bootstrap != null && overrides.skipConfirm && !authed;
+  const manualSetup =
+    !keyless && (agent ? !hasRealAppTarget : bootstrap != null && overrides.skipConfirm && !authed);
 
-  if (!keyless && !skipAuth) {
+  if (!keyless && !manualSetup) {
     bar();
     await authenticateAndLink(ctx.cwd, options.app);
   }
@@ -104,12 +114,15 @@ export async function init(options: InitOptions = {}) {
 
   if (alreadySetUp) {
     log.success("\nClerk is already set up in this project.");
+    if (agent && manualSetup) {
+      printBootstrapManualSetupInfo(ctx.framework.name);
+    }
     outro("Done");
     return;
   }
 
   bar();
-  if (skipAuth) {
+  if (manualSetup) {
     printBootstrapManualSetupInfo(ctx.framework.name);
   } else if (!keyless) {
     await pull({ file: ctx.envFile, cwd: ctx.cwd });
@@ -205,28 +218,35 @@ function printBootstrapNextSteps(
 function printBootstrapManualSetupInfo(frameworkName: string): void {
   const lines = [
     `\n  ${frameworkName} requires API keys — set them up manually:`,
-    "    clerk auth login",
-    "    clerk link",
+    "    clerk init --app <app_id>",
     "    clerk env pull",
   ];
   log.info(lines.map(dim).join("\n"));
 }
 
 // --- Keyless ---
 
-function resolveKeylessMode(
-  bootstrap: BootstrapResult | null,
-  ctx: ProjectContext,
-  authed: boolean,
-): boolean {
-  // Auto-keyless is scoped to bootstrap (new-project) flows only. For existing
-  // projects, fall through to the authenticated flow so `clerk init` still
-  // runs `authenticateAndLink` and pulls real keys — even when signed out the
-  // user gets a login prompt rather than being silently dropped into keyless
-  // (which would skip `env pull` and could overwrite permissive middleware).
-  if (!bootstrap) return false;
-
+function resolveKeylessMode({
+  agent,
+  bootstrap,
+  ctx,
+  authed,
+  hasRealAppTarget,
+}: {
+  agent: boolean;
+  bootstrap: BootstrapResult | null;
+  ctx: ProjectContext;
+  authed: boolean;
+  hasRealAppTarget: boolean;
+}): boolean {
   if (ctx.framework.supportsKeyless) {
+    if (agent) return !hasRealAppTarget;
+
+    // Auto-keyless is scoped to bootstrap (new-project) flows only in human
+    // mode. Existing projects keep the authenticated flow so real keys can be
+    // pulled unless an agent explicitly chooses keyless by omitting an app.
+    if (!bootstrap) return false;
+
     // Authenticated (OAuth token or CLERK_PLATFORM_API_KEY) — use the
     // authenticated flow so real keys get pulled into .env. Otherwise fall
     // back to keyless: the app runs on auto-generated dev keys and the user