fix(init): pull API keys into bootstrapped project subdirectory by rafa-thayto · Pull Request #195 · clerk/cli

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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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Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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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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After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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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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After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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Run ID: c8e77119-5905-46d7-b634-cca44502baec

📥 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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_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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Run ID: c8e77119-5905-46d7-b634-cca44502baec

📥 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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_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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Run ID: c8e77119-5905-46d7-b634-cca44502baec

📥 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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_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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@rafa-thayto has exceeded the limit for the number of commits that can be reviewed per hour. Please wait 52 minutes and 43 seconds before requesting another review.

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⌛ How to resolve this issue?

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🚦 How do rate limits work?

CodeRabbit enforces hourly rate limits for each developer per organization.

Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout.

Please see our FAQ for further information.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: c8e77119-5905-46d7-b634-cca44502baec

📥 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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❤️ Share

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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

Not sure what this means? Click here to learn what changesets are.

Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

Warning

Rate limit exceeded

@rafa-thayto has exceeded the limit for the number of commits that can be reviewed per hour. Please wait 52 minutes and 43 seconds before requesting another review.

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.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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_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto · 2026-04-21T16:10:52Z

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 · 2026-04-21T16:10:56Z

🦋 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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Click here if you're a maintainer who wants to add another changeset to this PR

coderabbitai · 2026-04-21T16:11:02Z

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Run ID: c8e77119-5905-46d7-b634-cca44502baec

📥 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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_{Comment @coderabbitai help to get the list of available commands and usage tips.}

After `clerk init` bootstraps a new project, the final `env pull` step resolved the linked profile via `process.cwd()` (still the parent directory), producing "No Clerk project linked to this directory" even though the freshly-created app was correctly linked under the subdir's absolute path. Thread `cwd` through `resolveAppContext` and `pull()` and pass `ctx.cwd` from init.

rafa-thayto mentioned this pull request Apr 21, 2026
fix(init,link): handle expired OAuth sessions gracefully #197
Closed
3 tasks

rafa-thayto requested a review from wyattjoh April 21, 2026 20:08

rafa-thayto force-pushed the rafa-thayto/init-improvements branch from 944e508 to 944c1cdCompare April 21, 2026 20:11

wyattjoh approved these changes Apr 21, 2026
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rafa-thayto merged commit 890137f into mainApr 21, 2026
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rafa-thayto deleted the rafa-thayto/init-improvements branch April 21, 2026 20:19

github-actionsBot mentioned this pull request Apr 21, 2026
ci(repo): Version Packages #181
Merged