Fix: Link command uses wrong directory during bootstrap flow

.changeset/fix-bootstrap-link-cwd.md

@@ -0,0 +1,5 @@
+---
+"clerk": patch
+---
+
+Fix link saving to wrong directory during bootstrap flow. When creating a new project via `clerk init`, the Clerk application link is now correctly saved to the new project directory instead of the parent directory.

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

@@ -114,7 +114,11 @@ describe("init", () => {
     await init({ yes: true });
 
     expect(loginMod.login).toHaveBeenCalledWith({ showNextSteps: false });
-    expect(linkMod.link).toHaveBeenCalledWith({ skipIfLinked: true, app: undefined });
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: undefined,
+      cwd: FAKE_CTX.cwd,
+    });
   });
 
   test("forwards --app to link when provided", async () => {
@@ -126,7 +130,11 @@ describe("init", () => {
 
     await init({ yes: true, app: "app_abc" });
 
-    expect(linkMod.link).toHaveBeenCalledWith({ skipIfLinked: true, app: "app_abc" });
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: "app_abc",
+      cwd: FAKE_CTX.cwd,
+    });
   });
 
   test("forwards --app to link when no profile exists", async () => {
@@ -136,7 +144,11 @@ describe("init", () => {
 
     await init({ yes: true, app: "app_abc" });
 
-    expect(linkMod.link).toHaveBeenCalledWith({ skipIfLinked: true, app: "app_abc" });
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: "app_abc",
+      cwd: FAKE_CTX.cwd,
+    });
   });
 
   test("agent mode runs existing-project flow without prompts", async () => {
@@ -571,7 +583,11 @@ describe("init", () => {
 
     await init({ yes: true });
 
-    expect(linkMod.link).toHaveBeenCalledWith({ skipIfLinked: true });
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: undefined,
+      cwd: "/tmp/fake",
+    });
     expect(pullMod.pull).not.toHaveBeenCalled();
     expect(heuristics.printKeylessInfo).not.toHaveBeenCalled();
     expect(skillsMod.installSkills).not.toHaveBeenCalled();
@@ -646,4 +662,28 @@ describe("init", () => {
 
     expect(pullMod.pull).toHaveBeenCalledWith({ file: ".env" });
   });
+
+  test("bootstrap passes project dir to link, not parent cwd", async () => {
+    setup({ email: "test@test.com" });
+
+    const bootstrapCtx = {
+      ...FAKE_CTX,
+      cwd: FAKE_BOOTSTRAP.projectDir,
+      existingClerk: false,
+    };
+
+    spyOn(context, "gatherContext").mockResolvedValueOnce(null).mockResolvedValueOnce(bootstrapCtx);
+    spyOn(scaffoldMod, "scaffold").mockResolvedValue({
+      actions: [{ type: "create", path: "app/layout.tsx", content: "", description: "" }],
+      postInstructions: [],
+    });
+
+    await init({ yes: true });
+
+    expect(linkMod.link).toHaveBeenCalledWith({
+      skipIfLinked: true,
+      app: undefined,
+      cwd: FAKE_BOOTSTRAP.projectDir,
+    });
+  });
 });

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

@@ -273,7 +273,7 @@ async function authenticateAndLink(cwd: string, app: string | undefined): Promis
     log.info(dim(label));
   }
 
-  await link({ skipIfLinked: true, app });
+  await link({ skipIfLinked: true, app, cwd });
 }
 
 // --- Detect & install ---

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

@@ -44,6 +44,7 @@ const CREATE_NEW_APP = "__create_new__";
 interface LinkOptions {
   app?: string;
   skipIfLinked?: boolean;
+  cwd?: string;
 }
 
 function appLabel(app: Application): string {
@@ -56,10 +57,10 @@ export async function link(options: LinkOptions = {}): Promise<void> {
     return;
   }
 
-  const cwd = process.cwd();
-  const repoRoot = await getGitRepoRoot();
-  const normalizedRemote = await getGitNormalizedRemote();
-  const repoId = await getGitRepoIdentifier();
+  const cwd = options.cwd ?? process.cwd();
+  const repoRoot = await getGitRepoRoot(cwd);
+  const normalizedRemote = await getGitNormalizedRemote(cwd);
+  const repoId = await getGitRepoIdentifier(cwd);
   const profileKey = normalizedRemote ?? repoId ?? cwd;
   const displayPath = repoRoot ?? cwd;
 

packages/cli-core/src/lib/autolink.ts

@@ -109,8 +109,8 @@ export async function autolink(
     `autolink: matched key from ${match.source} → app ${match.app.application_id} (${match.app.name ?? "unnamed"})`,
   );
 
-  const normalizedRemote = await getGitNormalizedRemote();
-  const repoId = await getGitRepoIdentifier();
+  const normalizedRemote = await getGitNormalizedRemote(cwd);
+  const repoId = await getGitRepoIdentifier(cwd);
   const profileKey = normalizedRemote ?? repoId ?? cwd;
 
   const devInstance = match.app.instances.find((i) => i.environment_type === "development");

packages/cli-core/src/lib/config.ts

@@ -169,7 +169,7 @@ export async function resolveProfile(cwd: string): Promise<
   const config = await readConfig();
 
   // Try normalized remote URL first (cross-clone matching)
-  const normalizedRemote = await getGitNormalizedRemote();
+  const normalizedRemote = await getGitNormalizedRemote(cwd);
   if (normalizedRemote && config.profiles[normalizedRemote]) {
     return {
       path: normalizedRemote,
@@ -182,7 +182,7 @@ export async function resolveProfile(cwd: string): Promise<
   const fallbackFields = normalizedRemote ? { availableRemote: normalizedRemote } : {};
 
   // Try git repo identifier (shared across worktrees, backward compat)
-  const repoId = await getGitRepoIdentifier();
+  const repoId = await getGitRepoIdentifier(cwd);
   if (repoId && config.profiles[repoId]) {
     return {
       path: repoId,

packages/cli-core/src/lib/git.ts

@@ -9,15 +9,25 @@ interface GitRepoInfo {
   normalizedRemote?: string;
 }
 
-let cached: GitRepoInfo | undefined | null = null;
+const cache = new Map<string, GitRepoInfo | undefined>();
 
-async function getGitRepoInfo(): Promise<GitRepoInfo | undefined> {
-  if (cached !== null) return cached ?? undefined;
+async function getGitRepoInfo(cwd?: string): Promise<GitRepoInfo | undefined> {
+  const key = cwd ?? process.cwd();
+  if (cache.has(key)) return cache.get(key);
+
+  let result;
+  try {
+    result = await $`git rev-parse --show-toplevel --git-common-dir`.cwd(key).quiet().nothrow();
+  } catch {
+    // Directory doesn't exist or other error (e.g., ENOENT)
+    log.debug(`git: rev-parse threw (cwd=${key})`);
+    cache.set(key, undefined);
+    return undefined;
+  }
 
-  const result = await $`git rev-parse --show-toplevel --git-common-dir`.quiet().nothrow();
   if (result.exitCode !== 0) {
     log.debug("git: not a git repository (git rev-parse failed)");
-    cached = undefined;
+    cache.set(key, undefined);
     return undefined;
   }
 
@@ -26,37 +36,44 @@ async function getGitRepoInfo(): Promise<GitRepoInfo | undefined> {
   const commonDir = lines[1];
   if (!toplevel || !commonDir) {
     log.debug("git: rev-parse returned no toplevel/commonDir");
-    cached = undefined;
+    cache.set(key, undefined);
     return undefined;
   }
 
   // Fetch remote URL (non-blocking since rev-parse already succeeded)
-  const remoteResult = await $`git remote get-url origin`.quiet().nothrow();
-  const rawRemote = remoteResult.exitCode === 0 ? remoteResult.text().trim() : undefined;
+  let rawRemote: string | undefined;
+  try {
+    const remoteResult = await $`git remote get-url origin`.cwd(key).quiet().nothrow();
+    rawRemote = remoteResult.exitCode === 0 ? remoteResult.text().trim() : undefined;
+  } catch {
+    // Directory error or git command failed
+    rawRemote = undefined;
+  }
 
-  cached = {
+  const info = {
     toplevel,
     commonDir: resolve(toplevel, commonDir),
     normalizedRemote: rawRemote ? normalizeGitRemoteUrl(rawRemote) : undefined,
   };
+  cache.set(key, info);
   log.debug(
-    `git: toplevel=${cached.toplevel}, commonDir=${cached.commonDir}, remote=${cached.normalizedRemote ?? "<none>"}`,
+    `git: toplevel=${info.toplevel}, commonDir=${info.commonDir}, remote=${info.normalizedRemote ?? "<none>"}`,
   );
-  return cached;
+  return info;
 }
 
-export async function getGitRepoRoot(): Promise<string | undefined> {
-  const info = await getGitRepoInfo();
+export async function getGitRepoRoot(cwd?: string): Promise<string | undefined> {
+  const info = await getGitRepoInfo(cwd);
   return info?.toplevel;
 }
 
-export async function getGitRepoIdentifier(): Promise<string | undefined> {
-  const info = await getGitRepoInfo();
+export async function getGitRepoIdentifier(cwd?: string): Promise<string | undefined> {
+  const info = await getGitRepoInfo(cwd);
   return info?.commonDir;
 }
 
-export async function getGitNormalizedRemote(): Promise<string | undefined> {
-  const info = await getGitRepoInfo();
+export async function getGitNormalizedRemote(cwd?: string): Promise<string | undefined> {
+  const info = await getGitRepoInfo(cwd);
   return info?.normalizedRemote;
 }