From b57d68b176e669c2dfcd9cda51d6600b9b5d76f2 Mon Sep 17 00:00:00 2001
From: Ben Sandler <bensandler@stripe.com>
Date: Thu, 10 Sep 2026 17:15:01 -0400
Subject: [PATCH 1/5] Prevent MCP registration from launching the wrong npm
 package

- Incur confuses the link-cli executable with its npm package, generating npx link-cli --mcp instead of @stripe/link-cli and potentially inheriting package references from project metadata.
- Set the default MCP command from the trusted package name and version embedded at build time.
- Add an isolated registration regression test and repair guidance for existing MCP registrations.
- Leave the separate unsafe skills suggestion path for the upstream Incur follow-up.

Committed-By-Agent: codex
Co-authored-by: codex <noreply@openai.com>
---
 .changeset/safe-mcp-package.md                |  6 ++
 .../src/__tests__/mcp-registration.test.ts    | 59 +++++++++++++++++++
 packages/cli/src/cli.tsx                      |  3 +
 3 files changed, 68 insertions(+)
 create mode 100644 .changeset/safe-mcp-package.md
 create mode 100644 packages/cli/src/__tests__/mcp-registration.test.ts

diff --git a/.changeset/safe-mcp-package.md b/.changeset/safe-mcp-package.md
new file mode 100644
index 00000000..6aec2d11
--- /dev/null
+++ b/.changeset/safe-mcp-package.md
@@ -0,0 +1,6 @@
+---
+'@stripe/link-cli': patch
+---
+
+Register the MCP server with the versioned `@stripe/link-cli` package.
+Existing MCP registrations are not updated automatically; rerun `link-cli mcp add` after upgrading to replace the generated `link-cli` entry.
diff --git a/packages/cli/src/__tests__/mcp-registration.test.ts b/packages/cli/src/__tests__/mcp-registration.test.ts
new file mode 100644
index 00000000..2a5a1b4a
--- /dev/null
+++ b/packages/cli/src/__tests__/mcp-registration.test.ts
@@ -0,0 +1,59 @@
+import { execFile } from 'node:child_process';
+import {
+  chmodSync,
+  mkdtempSync,
+  readFileSync,
+  rmSync,
+  writeFileSync,
+} from 'node:fs';
+import os from 'node:os';
+import path from 'node:path';
+import { promisify } from 'node:util';
+import { afterEach, describe, expect, it } from 'vitest';
+
+const execFileAsync = promisify(execFile);
+const CLI_PATH = new URL('../../dist/cli.js', import.meta.url).pathname;
+const PACKAGE = JSON.parse(
+  readFileSync(new URL('../../package.json', import.meta.url), 'utf8'),
+) as { version: string };
+
+let testDirectory: string | undefined;
+
+afterEach(() => {
+  if (testDirectory) rmSync(testDirectory, { force: true, recursive: true });
+  testDirectory = undefined;
+});
+
+describe('MCP registration', () => {
+  it('registers the versioned scoped package', async () => {
+    testDirectory = mkdtempSync(path.join(os.tmpdir(), 'link-cli-mcp-test-'));
+    const capturePath = path.join(testDirectory, 'arguments.json');
+    const npxPath = path.join(testDirectory, 'npx');
+    writeFileSync(
+      npxPath,
+      `#!/usr/bin/env node
+import { writeFileSync } from 'node:fs';
+writeFileSync(process.env.LINK_MCP_TEST_CAPTURE, JSON.stringify(process.argv.slice(2)));
+`,
+    );
+    chmodSync(npxPath, 0o755);
+
+    await execFileAsync(
+      process.execPath,
+      [CLI_PATH, 'mcp', 'add', '--agent', 'cursor'],
+      {
+        env: {
+          ...process.env,
+          LINK_MCP_TEST_CAPTURE: capturePath,
+          npm_config_user_agent: 'npm/10.0.0 node/v22.0.0',
+          PATH: `${testDirectory}:${process.env.PATH}`,
+        },
+      },
+    );
+
+    const argumentsPassed = JSON.parse(readFileSync(capturePath, 'utf8'));
+    expect(argumentsPassed).toContain(
+      `npx @stripe/link-cli@${PACKAGE.version} --mcp`,
+    );
+  });
+});
diff --git a/packages/cli/src/cli.tsx b/packages/cli/src/cli.tsx
index d33a2fd0..0298973a 100644
--- a/packages/cli/src/cli.tsx
+++ b/packages/cli/src/cli.tsx
@@ -67,6 +67,9 @@ const cli = Cli.create('link-cli', {
   description:
     'Create a secure, one-time payment credential from a Link wallet to let agents complete purchases on behalf of users.',
   version: cliVersion,
+  mcp: {
+    command: `npx ${cliName}@${cliVersion} --mcp`,
+  },
   sync: {
     include: ['skills/*'],
   },

From 3113a4b9b4ab2fb8a4910eaad6748be68538fb6e Mon Sep 17 00:00:00 2001
From: Ben Sandler <bensandler@stripe.com>
Date: Thu, 10 Sep 2026 22:28:34 -0400
Subject: [PATCH 2/5] Preserve package runners in MCP registration

- Hardcoded npx broke MCP registration in Bun- and pnpm-only environments.
- Mirror Incur runner precedence while retaining the scoped, versioned Link CLI package.
- Replace the subprocess regression test with compact npm, pnpm, Bun, and precedence coverage.

Committed-By-Agent: codex
Co-authored-by: codex <noreply@openai.com>
---
 .changeset/safe-mcp-package.md                |  6 +-
 .../src/__tests__/mcp-registration.test.ts    | 59 -------------------
 packages/cli/src/cli.tsx                      |  3 +-
 .../utils/__tests__/package-runner.test.ts    | 11 ++++
 packages/cli/src/utils/package-runner.ts      | 31 ++++++++++
 5 files changed, 48 insertions(+), 62 deletions(-)
 delete mode 100644 packages/cli/src/__tests__/mcp-registration.test.ts
 create mode 100644 packages/cli/src/utils/__tests__/package-runner.test.ts
 create mode 100644 packages/cli/src/utils/package-runner.ts

diff --git a/.changeset/safe-mcp-package.md b/.changeset/safe-mcp-package.md
index 6aec2d11..2fd60f36 100644
--- a/.changeset/safe-mcp-package.md
+++ b/.changeset/safe-mcp-package.md
@@ -2,5 +2,7 @@
 '@stripe/link-cli': patch
 ---
 
-Register the MCP server with the versioned `@stripe/link-cli` package.
-Existing MCP registrations are not updated automatically; rerun `link-cli mcp add` after upgrading to replace the generated `link-cli` entry.
+Register the MCP server with the detected package runner and versioned
+`@stripe/link-cli` package. Existing MCP registrations are not updated
+automatically; rerun `link-cli mcp add` after upgrading to replace the generated
+`link-cli` entry.
diff --git a/packages/cli/src/__tests__/mcp-registration.test.ts b/packages/cli/src/__tests__/mcp-registration.test.ts
deleted file mode 100644
index 2a5a1b4a..00000000
--- a/packages/cli/src/__tests__/mcp-registration.test.ts
+++ /dev/null
@@ -1,59 +0,0 @@
-import { execFile } from 'node:child_process';
-import {
-  chmodSync,
-  mkdtempSync,
-  readFileSync,
-  rmSync,
-  writeFileSync,
-} from 'node:fs';
-import os from 'node:os';
-import path from 'node:path';
-import { promisify } from 'node:util';
-import { afterEach, describe, expect, it } from 'vitest';
-
-const execFileAsync = promisify(execFile);
-const CLI_PATH = new URL('../../dist/cli.js', import.meta.url).pathname;
-const PACKAGE = JSON.parse(
-  readFileSync(new URL('../../package.json', import.meta.url), 'utf8'),
-) as { version: string };
-
-let testDirectory: string | undefined;
-
-afterEach(() => {
-  if (testDirectory) rmSync(testDirectory, { force: true, recursive: true });
-  testDirectory = undefined;
-});
-
-describe('MCP registration', () => {
-  it('registers the versioned scoped package', async () => {
-    testDirectory = mkdtempSync(path.join(os.tmpdir(), 'link-cli-mcp-test-'));
-    const capturePath = path.join(testDirectory, 'arguments.json');
-    const npxPath = path.join(testDirectory, 'npx');
-    writeFileSync(
-      npxPath,
-      `#!/usr/bin/env node
-import { writeFileSync } from 'node:fs';
-writeFileSync(process.env.LINK_MCP_TEST_CAPTURE, JSON.stringify(process.argv.slice(2)));
-`,
-    );
-    chmodSync(npxPath, 0o755);
-
-    await execFileAsync(
-      process.execPath,
-      [CLI_PATH, 'mcp', 'add', '--agent', 'cursor'],
-      {
-        env: {
-          ...process.env,
-          LINK_MCP_TEST_CAPTURE: capturePath,
-          npm_config_user_agent: 'npm/10.0.0 node/v22.0.0',
-          PATH: `${testDirectory}:${process.env.PATH}`,
-        },
-      },
-    );
-
-    const argumentsPassed = JSON.parse(readFileSync(capturePath, 'utf8'));
-    expect(argumentsPassed).toContain(
-      `npx @stripe/link-cli@${PACKAGE.version} --mcp`,
-    );
-  });
-});
diff --git a/packages/cli/src/cli.tsx b/packages/cli/src/cli.tsx
index 0298973a..8f1a1f1d 100644
--- a/packages/cli/src/cli.tsx
+++ b/packages/cli/src/cli.tsx
@@ -14,6 +14,7 @@ import { createSpendRequestCli } from './commands/spend-request';
 import { createTransactionsCli } from './commands/transactions';
 import { createUserInfoCli } from './commands/user-info';
 import { createWebBotAuthCli } from './commands/web-bot-auth';
+import { detectPackageRunner } from './utils/package-runner';
 import { ResourceFactory } from './utils/resource-factory';
 import {
   createAgentUpdateInfoProvider,
@@ -68,7 +69,7 @@ const cli = Cli.create('link-cli', {
     'Create a secure, one-time payment credential from a Link wallet to let agents complete purchases on behalf of users.',
   version: cliVersion,
   mcp: {
-    command: `npx ${cliName}@${cliVersion} --mcp`,
+    command: `${detectPackageRunner()} ${cliName}@${cliVersion} --mcp`,
   },
   sync: {
     include: ['skills/*'],
diff --git a/packages/cli/src/utils/__tests__/package-runner.test.ts b/packages/cli/src/utils/__tests__/package-runner.test.ts
new file mode 100644
index 00000000..c4e31675
--- /dev/null
+++ b/packages/cli/src/utils/__tests__/package-runner.test.ts
@@ -0,0 +1,11 @@
+import { expect, it } from 'vitest';
+import { detectPackageRunner } from '../package-runner';
+
+it.each([
+  ['npm user agent', ['npm/10.0.0'], 'npx'],
+  ['npm before a pnpm executable', ['npm/10.0.0', '/bin/pnpm'], 'npx'],
+  ['pnpm executable', ['', '/bin/pnpm.cjs'], 'pnpx'],
+  ['Bun entrypoint', ['', '', '/tmp/.bun/bin/cli'], 'bunx'],
+])('detects the package runner from the %s', (_, hints, expected) => {
+  expect(detectPackageRunner(hints)).toBe(expected);
+});
diff --git a/packages/cli/src/utils/package-runner.ts b/packages/cli/src/utils/package-runner.ts
new file mode 100644
index 00000000..741d1cec
--- /dev/null
+++ b/packages/cli/src/utils/package-runner.ts
@@ -0,0 +1,31 @@
+import { realpathSync } from 'node:fs';
+
+function runnerFromHint(value: string) {
+  if (value.includes('pnpm')) return 'pnpx';
+  if (value.includes('bun')) return 'bunx';
+  if (value.includes('npm')) return 'npx';
+}
+
+// Mirrors Incur's unexported detector because `mcp.command` replaces its default command.
+export function detectPackageRunner(hints?: readonly string[]) {
+  if (!hints) {
+    const userAgent = process.env.npm_config_user_agent ?? '';
+    let entry = process.argv[1] ?? '';
+    try {
+      entry = realpathSync(entry);
+    } catch {}
+
+    hints = [
+      /pnpm|bun/.test(userAgent) || userAgent.startsWith('npm/')
+        ? userAgent
+        : '',
+      process.env.npm_execpath ?? '',
+      /(?:\/\.pnpm\/|\\\.pnpm\\)/.test(entry)
+        ? 'pnpm'
+        : /(?:\/\.bun\/|\\bun\\)/.test(entry)
+          ? 'bun'
+          : '',
+    ];
+  }
+  return hints.map(runnerFromHint).find(Boolean) ?? 'npx';
+}

From d18d325e468529c9be0e5ce2b9b5b578ab22c7c7 Mon Sep 17 00:00:00 2001
From: Ben Sandler <bensandler@stripe.com>
Date: Thu, 10 Sep 2026 22:39:08 -0400
Subject: [PATCH 3/5] Fix package runner lint

- Use a local resolved hints variable to avoid reassigning the function parameter.
- Preserve existing package-runner detection behavior and precedence.

Committed-By-Agent: codex
Co-authored-by: codex <noreply@openai.com>
---
 packages/cli/src/utils/package-runner.ts | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/packages/cli/src/utils/package-runner.ts b/packages/cli/src/utils/package-runner.ts
index 741d1cec..dd0c1123 100644
--- a/packages/cli/src/utils/package-runner.ts
+++ b/packages/cli/src/utils/package-runner.ts
@@ -8,14 +8,15 @@ function runnerFromHint(value: string) {
 
 // Mirrors Incur's unexported detector because `mcp.command` replaces its default command.
 export function detectPackageRunner(hints?: readonly string[]) {
-  if (!hints) {
+  let resolvedHints = hints;
+  if (!resolvedHints) {
     const userAgent = process.env.npm_config_user_agent ?? '';
     let entry = process.argv[1] ?? '';
     try {
       entry = realpathSync(entry);
     } catch {}
 
-    hints = [
+    resolvedHints = [
       /pnpm|bun/.test(userAgent) || userAgent.startsWith('npm/')
         ? userAgent
         : '',
@@ -27,5 +28,5 @@ export function detectPackageRunner(hints?: readonly string[]) {
           : '',
     ];
   }
-  return hints.map(runnerFromHint).find(Boolean) ?? 'npx';
+  return resolvedHints.map(runnerFromHint).find(Boolean) ?? 'npx';
 }

From 1661d74e43cf5bfd3ec7a051abaa93144060ab6d Mon Sep 17 00:00:00 2001
From: Ben Sandler <bensandler@stripe.com>
Date: Thu, 10 Sep 2026 22:57:11 -0400
Subject: [PATCH 4/5] Preserve standalone MCP execution

- Register Node standalone builds with their current executable path.
- Keep the detected package runner and pinned scoped package for managed installs.
- Cover standalone registration and document the corrected behavior.

Committed-By-Agent: codex
Co-authored-by: codex <noreply@openai.com>
---
 .changeset/safe-mcp-package.md                   |  8 ++++----
 packages/cli/src/cli.tsx                         |  4 ++--
 .../src/utils/__tests__/package-runner.test.ts   | 11 ++++++++++-
 packages/cli/src/utils/package-runner.ts         | 16 ++++++++++++++++
 4 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/.changeset/safe-mcp-package.md b/.changeset/safe-mcp-package.md
index 2fd60f36..e66ed004 100644
--- a/.changeset/safe-mcp-package.md
+++ b/.changeset/safe-mcp-package.md
@@ -2,7 +2,7 @@
 '@stripe/link-cli': patch
 ---
 
-Register the MCP server with the detected package runner and versioned
-`@stripe/link-cli` package. Existing MCP registrations are not updated
-automatically; rerun `link-cli mcp add` after upgrading to replace the generated
-`link-cli` entry.
+Register the MCP server with its standalone executable when applicable, or the
+detected package runner and versioned `@stripe/link-cli` package. Existing MCP
+registrations are not updated automatically; rerun `link-cli mcp add` after
+upgrading to replace the generated `link-cli` entry.
diff --git a/packages/cli/src/cli.tsx b/packages/cli/src/cli.tsx
index 8f1a1f1d..ecdc577b 100644
--- a/packages/cli/src/cli.tsx
+++ b/packages/cli/src/cli.tsx
@@ -14,7 +14,7 @@ import { createSpendRequestCli } from './commands/spend-request';
 import { createTransactionsCli } from './commands/transactions';
 import { createUserInfoCli } from './commands/user-info';
 import { createWebBotAuthCli } from './commands/web-bot-auth';
-import { detectPackageRunner } from './utils/package-runner';
+import { buildMcpCommand } from './utils/package-runner';
 import { ResourceFactory } from './utils/resource-factory';
 import {
   createAgentUpdateInfoProvider,
@@ -69,7 +69,7 @@ const cli = Cli.create('link-cli', {
     'Create a secure, one-time payment credential from a Link wallet to let agents complete purchases on behalf of users.',
   version: cliVersion,
   mcp: {
-    command: `${detectPackageRunner()} ${cliName}@${cliVersion} --mcp`,
+    command: buildMcpCommand(cliName, cliVersion),
   },
   sync: {
     include: ['skills/*'],
diff --git a/packages/cli/src/utils/__tests__/package-runner.test.ts b/packages/cli/src/utils/__tests__/package-runner.test.ts
index c4e31675..03e79a55 100644
--- a/packages/cli/src/utils/__tests__/package-runner.test.ts
+++ b/packages/cli/src/utils/__tests__/package-runner.test.ts
@@ -1,5 +1,5 @@
 import { expect, it } from 'vitest';
-import { detectPackageRunner } from '../package-runner';
+import { buildMcpCommand, detectPackageRunner } from '../package-runner';
 
 it.each([
   ['npm user agent', ['npm/10.0.0'], 'npx'],
@@ -9,3 +9,12 @@ it.each([
 ])('detects the package runner from the %s', (_, hints, expected) => {
   expect(detectPackageRunner(hints)).toBe(expected);
 });
+
+it('uses the current executable for a standalone SEA', () => {
+  expect(
+    buildMcpCommand('@stripe/link-cli', '1.2.3', {
+      sea: true,
+      executable: '/Applications/Link CLI/link-cli',
+    }),
+  ).toBe('"/Applications/Link CLI/link-cli" --mcp');
+});
diff --git a/packages/cli/src/utils/package-runner.ts b/packages/cli/src/utils/package-runner.ts
index dd0c1123..6a0be07a 100644
--- a/packages/cli/src/utils/package-runner.ts
+++ b/packages/cli/src/utils/package-runner.ts
@@ -1,4 +1,5 @@
 import { realpathSync } from 'node:fs';
+import { isSea } from 'node:sea';
 
 function runnerFromHint(value: string) {
   if (value.includes('pnpm')) return 'pnpx';
@@ -30,3 +31,18 @@ export function detectPackageRunner(hints?: readonly string[]) {
   }
   return resolvedHints.map(runnerFromHint).find(Boolean) ?? 'npx';
 }
+
+export function buildMcpCommand(
+  packageName: string,
+  version: string,
+  {
+    sea = isSea(),
+    executable = process.execPath,
+  }: {
+    sea?: boolean;
+    executable?: string;
+  } = {},
+) {
+  if (sea) return `"${executable.replaceAll('"', '\\"')}" --mcp`;
+  return `${detectPackageRunner()} ${packageName}@${version} --mcp`;
+}

From 259c015e96a3827c7bdb5990621e8c3f54369cd2 Mon Sep 17 00:00:00 2001
From: Ben Sandler <bensandler@stripe.com>
Date: Thu, 10 Sep 2026 23:00:24 -0400
Subject: [PATCH 5/5] Avoid a SEA runtime import in the CLI bundle

- Detect standalone execution by comparing the resolved entrypoint and executable paths.
- Avoid the node:sea import that the regular CLI bundle rewrites incorrectly.
- Preserve absolute executable registration with the focused standalone regression.

Committed-By-Agent: codex
Co-authored-by: codex <noreply@openai.com>
---
 .../cli/src/utils/__tests__/package-runner.test.ts   |  2 +-
 packages/cli/src/utils/package-runner.ts             | 12 ++++++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/packages/cli/src/utils/__tests__/package-runner.test.ts b/packages/cli/src/utils/__tests__/package-runner.test.ts
index 03e79a55..21a0200c 100644
--- a/packages/cli/src/utils/__tests__/package-runner.test.ts
+++ b/packages/cli/src/utils/__tests__/package-runner.test.ts
@@ -13,7 +13,7 @@ it.each([
 it('uses the current executable for a standalone SEA', () => {
   expect(
     buildMcpCommand('@stripe/link-cli', '1.2.3', {
-      sea: true,
+      entry: '/Applications/Link CLI/link-cli',
       executable: '/Applications/Link CLI/link-cli',
     }),
   ).toBe('"/Applications/Link CLI/link-cli" --mcp');
diff --git a/packages/cli/src/utils/package-runner.ts b/packages/cli/src/utils/package-runner.ts
index 6a0be07a..f3c26cec 100644
--- a/packages/cli/src/utils/package-runner.ts
+++ b/packages/cli/src/utils/package-runner.ts
@@ -1,5 +1,4 @@
 import { realpathSync } from 'node:fs';
-import { isSea } from 'node:sea';
 
 function runnerFromHint(value: string) {
   if (value.includes('pnpm')) return 'pnpx';
@@ -36,13 +35,18 @@ export function buildMcpCommand(
   packageName: string,
   version: string,
   {
-    sea = isSea(),
+    entry = process.argv[1],
     executable = process.execPath,
   }: {
-    sea?: boolean;
+    entry?: string;
     executable?: string;
   } = {},
 ) {
-  if (sea) return `"${executable.replaceAll('"', '\\"')}" --mcp`;
+  let standalone = entry === executable;
+  try {
+    standalone = realpathSync(entry ?? '') === realpathSync(executable);
+  } catch {}
+
+  if (standalone) return `"${executable.replaceAll('"', '\\"')}" --mcp`;
   return `${detectPackageRunner()} ${packageName}@${version} --mcp`;
 }