fix(init): pull API keys into bootstrapped project subdirectory

[rafa-thayto]

Summary

• When clerk init bootstraps a new project in a subdirectory and then runs env pull at the end, it fails with:

  error: No Clerk project linked to this directory.
  Either:
    - Run `clerk link` from your project directory
    - Pass --app <app_id> to target an app directly
  

  even though the Clerk app was just linked to the freshly-created subdirectory. Result: ✓ Clerk has been set up prints, then the command errors and .env.local is left without real API keys.

• Root cause: pull() and resolveAppContext() both hardcoded process.cwd(), which is still the parent directory (init never chdirs). The profile was correctly written under the subdir path by clerk link, but the subsequent lookup walked up from the parent and never found it.

• Fix: thread cwd as an optional parameter through resolveAppContext() and pull() (defaulting to process.cwd() for existing callers), pass ctx.cwd from init, and extract a shared AppContextOptions interface so EnvPullOptions extends it instead of redeclaring the fields. Also parallelizes the two independent awaits at the top of pull() with Promise.all.

Test plan

• bun run typecheck, bun run lint, bun run format:check, bun run test — all green (72 test files pass)
• New regression test in packages/cli-core/src/commands/env/pull.test.ts that passes cwd pointing at a directory distinct from process.cwd() and asserts the keys are written inside that directory (and not in process.cwd())
• New unit test in packages/cli-core/src/lib/config.test.ts covering resolveAppContext({ cwd }) finding profiles keyed by the explicit path
• Updated existing init assertion to verify pull is called with { file, cwd: ctx.cwd }
• Manual end-to-end: mkdir /tmp/foo && cd /tmp/foo && clerk init, pick TanStack Start + create new Clerk app — verify flow ends without error and <project>/.env.local contains real keys

[changeset-bot]

🦋 Changeset detected

Latest commit: 944c1cd

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
clerk	Patch

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📥 Commits

Reviewing files that changed from the base of the PR and between 9abc17e and 944c1cd.

📒 Files selected for processing (7)

• .changeset/init-improvements.md
• packages/cli-core/src/commands/env/pull.test.ts
• packages/cli-core/src/commands/env/pull.ts
• packages/cli-core/src/commands/init/index.test.ts
• packages/cli-core/src/commands/init/index.ts
• packages/cli-core/src/lib/config.test.ts
• packages/cli-core/src/lib/config.ts

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