feat(init): integrate native iOS setup

[seanperez29]

Summary

• expose native iOS setup through the normal clerk init framework-detection and application-linking flow
• coordinate local planning, user approval, transactional project changes, remote reconciliation, and final verification
• add dry-run, target selection, App ID Prefix resolution, optional AuthView setup, and optional Sign in with Apple setup
• keep agent mode deterministic while supporting the ordinary no-argument interactive experience
• add compiled-CLI, fixture, integration, and end-to-end coverage for the public workflow
• offer a target picker for interactive init and dry runs when several apps exist; carry the chosen target through planning and scaffolding, with cancellation before setup or authentication

Scope

This is the public integration layer connecting authentication and application selection to the local and remote capabilities in the preceding PRs.

It does not add Doctor diagnostics, macOS support, or Xcode JSON project-format support; those are isolated in later stack layers. Dry-run remains local and read-only, and local and remote mutations retain separate planning, approval, and verification boundaries.

A sole app target remains automatic. Explicit --target bypasses the picker. Agent mode, --yes, JSON output, and redirected input/output preserve the existing ambiguity response; none guesses a target. The picker uses exhaustive discovery and retains all later safety checks, including refusals for colliding target IDs across copied projects.

Validation

Current head: 50464d8360933608167d8bc6652d86c6a9e91662.

• Formatting, lint, typechecking, git diff --check, and all 3,903 unit tests passed.
• Integrated head 2aed604b passed all 4,315 unit tests and compilation. All seven updated branch heads passed local checks independently; feat(init): add iOS project inspection foundations #431 and feat(init): add transactional native iOS mutation engines #453 are unchanged.
• Forty new regressions cover prepared-domain validation, source ownership, atomic retry records, prefix casing, entitlement ownership, JSON document/package ambiguity, platform drift, and equivalent file paths.
• All 36 PBX/JSON corpus scenarios passed dry run, apply, unchanged rerun, and read-only Doctor assertions; all 40 unsigned simulator/macOS builds passed. The two custom-runtime existing-domain cases explicitly verify the dirty-file guard before rerunning unchanged with --allow-dirty.
• Toolchains: Xcode 26.5 (17F42) for PBX and Xcode 27.2 beta (27B5019j) for JSON. Corpus APIs used local GET-only stubs; no live backend writes were performed.
• Credential-backed E2E could not start because the current 1Password account cannot access the AI Enablement vault. It remains an outstanding release check, not a passing or failing test. GitHub CI was not queried or awaited; signed-device Apple sign-in was not rerun.
• Detailed local evidence: clerk-cli-real-xcode-corpus/reports/2026-09-25-coderabbit-five.md. Prior conditional SwiftUI-root and signing-output validation is recorded in the earlier reports.

Stack

1. feat(init): add iOS project inspection foundations #431 — native Apple project inspection foundations
2. feat(init): add transactional native iOS mutation engines #453 — transactional local mutation engines
3. feat(init): compose native iOS local setup #489 — native iOS local setup orchestration
4. feat(init): reconcile native iOS backend configuration #454 — native iOS backend reconciliation
5. feat(init): integrate native iOS setup #490 — public native iOS init integration
6. feat(doctor): add native iOS diagnostics #455 — native iOS Doctor diagnostics
7. feat(native): add macOS setup and diagnostics #486 — macOS setup and diagnostics
8. feat(init): support Xcode JSON project format #488 — Xcode JSON project format
9. fix(init): improve established Apple app setup and interactive flow #493 — established app operation gates and neutral entitlement ownership

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

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Run ID: c8f7badb-e096-42dd-8fa3-9f430f76df41

📥 Commits

Reviewing files that changed from the base of the PR and between 9cddf69 and 1eb63b9.

📒 Files selected for processing (32)

• .changeset/ios-native-init-integration.md
• packages/cli-core/src/cli-program.ts
• packages/cli-core/src/commands/init/README.md
• packages/cli-core/src/commands/init/frameworks/ios.test.ts
• packages/cli-core/src/commands/init/frameworks/ios.ts
• packages/cli-core/src/commands/init/frameworks/types.ts
• packages/cli-core/src/commands/init/index-ios.test.ts
• packages/cli-core/src/commands/init/index.test.ts
• packages/cli-core/src/commands/init/index.ts
• packages/cli-core/src/commands/init/ios/apply-cli-runtime.test.ts
• packages/cli-core/src/commands/init/ios/apply-cli.test-helpers.ts
• packages/cli-core/src/commands/init/ios/apply-cli.test.ts
• packages/cli-core/src/commands/init/ios/compiled-cli.test.ts
• packages/cli-core/src/commands/init/ios/coordinator.ts
• packages/cli-core/src/commands/init/ios/dry-run.test.ts
• packages/cli-core/src/commands/init/ios/target-picker.test.ts
• packages/cli-core/src/commands/init/ios/target-picker.ts
• packages/cli-core/src/commands/init/strategy.test.ts
• packages/cli-core/src/commands/link/index.test.ts
• packages/cli-core/src/commands/link/index.ts
• packages/cli-core/src/lib/app-picker.ts
• packages/cli-core/src/lib/framework.ts
• packages/cli-core/src/lib/telemetry.ts
• packages/cli-core/src/test/integration/agent-mode.test.ts
• packages/cli-core/src/test/lib/init-harness.ts
• test/e2e/fixtures/ios/MyApp.xcodeproj/project.pbxproj
• test/e2e/fixtures/ios/MyApp/ContentView.swift
• test/e2e/fixtures/ios/MyApp/MyApp.entitlements
• test/e2e/fixtures/ios/MyApp/MyAppApp.swift
• test/e2e/fixtures/ios/README.md
• test/e2e/lib/fixture-setup.ts
• test/e2e/native-init.test.ts

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• clerk/clerk_go (manual)
• clerk/dashboard (manual)
• clerk/accounts (manual)
• clerk/backoffice (manual)
• clerk/clerk (manual)
• clerk/clerk-docs (manual)
• clerk/cloudflare-workers (manual)
• clerk/javascript (auto-detected)

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📝 Walkthrough

Walkthrough

clerk init now supports native iOS project inspection and setup, including read-only dry runs, target selection, Xcode package and Swift configuration, and optional prebuilt Auth UI or Sign in with Apple. The flow validates authentication and application links before remote setup, and uses local and remote setup phases. The change also updates application-linking controls, iOS guidance, tests, and end-to-end fixtures.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Suggested reviewers: rafa-thayto

Merge Risk: ⚪ Minimal · up to 1eb63

Native iOS setup is now part of clerk init, with dry-run, target selection, and optional Apple and prebuilt UI setup. It has extensive test coverage, and no concrete defect is known at the current head. The change appears ready to merge after normal checks.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 22.22% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 63 functions across 27 files. (5 skipped:…	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly and concisely describes the main change: integrating native iOS setup into init.
Description check	✅ Passed	The description directly explains the native iOS init integration, its capabilities, scope, and validation.

Full details: Docstring Coverage

Explanation

Docstring coverage is 22.22% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 63 functions across 27 files. (5 skipped: 5 unsupported.)

• Fix all pre-merge checks with AI

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Commit to this branch
• Create a new PR

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[changeset-bot]

🦋 Changeset detected

Latest commit: edb8770

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

This PR includes changesets to release 1 package

Name	Type
clerk	Minor

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