[codex] Add onboarding journal setup and initial index default

[cleak]

Summary

This updates Tempyr onboarding so the interactive flow makes both setup concerns explicit:

• default the interactive init wizard to run the initial structural index rebuild after setup
• add a dedicated journal setup page with toggles for journal auto-publish, journal ref fetch configuration, and local journal layout bootstrap
• route the selected journal setup choices through tempyr init instead of silently applying the old implicit behavior
• add focused tests for the new wizard defaults, journal toggles, index rebuild side effect, and journal layout bootstrap

Why

Users could complete onboarding without getting an initial index, and journal setup was inferred from repo visibility without an explicit onboarding prompt. The wizard now shows those choices directly, while non-interactive init stays conservative about potentially expensive index work.

Validation

• cargo fmt --check
• cargo clippy --all-targets -- -D warnings
• cargo test -p tempyr-cli
• cargo test
• git diff --check

Summary by CodeRabbit

• New Features

  • Added a dedicated journal setup step to onboarding with interactive toggles for enabling the journal, fetch refspec, and layout bootstrap.
  • Project init now applies journal setup choices and may bootstrap journal layout during init.

• Bug Fixes

  • Journal-related defaults now derive from repository context and are consistently applied in non-interactive flows.

• Tests

  • Added coverage for initial index rebuild and journal bootstrap/idempotency during init.

• Documentation

  • Updated test docs/comments describing journal lifecycle and bootstrap behavior.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 94edcd71-1542-49b6-9e69-e2c809ddf16f

📥 Commits

Reviewing files that changed from the base of the PR and between d6e0d6d and 801a8eb.

📒 Files selected for processing (3)

• crates/tempyr-cli/src/commands/init.rs
• crates/tempyr-cli/src/commands/onboarding.rs
• crates/tempyr-cli/tests/integration.rs

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📝 Walkthrough

Walkthrough

Init now computes journal setup defaults from repository context and passes them into onboarding and non-interactive flows. Journal configuration is applied during project initialization via a new apply_journal_init path; onboarding gains a dedicated JournalSetup page and selections are persisted into initialization logic and tests.

Changes

Journal Setup in Init & Onboarding

Layer / File(s)	Summary
Data Shape crates/tempyr-cli/src/commands/onboarding.rs	Adds JournalSetupDefaults (enable_journal, configure_journal_fetch_refspec, bootstrap_journal_layout) and extends OnboardingSelections with the same three booleans.
Default Computation crates/tempyr-cli/src/commands/init.rs	Adds journal_setup_defaults(root: &Path) and is_inside_git_repo(root: &Path) to derive journal defaults from git presence/visibility.
Wizard Init & Routing crates/tempyr-cli/src/commands/onboarding.rs	run(...) now accepts journal_defaults; WizardState gains journal_index; pages always include Page::JournalSetup; new_with_journal_defaults initializes selections from defaults.
Interaction Handling crates/tempyr-cli/src/commands/onboarding.rs	Adds handle_journal_setup, toggle_journal_option, and journal option enums to navigate and toggle the three journal choices.
Rendering crates/tempyr-cli/src/commands/onboarding.rs	Adds render_journal_setup, updates header/footer text and welcome list, and shows journal details in the Review page.
Init Integration crates/tempyr-cli/src/commands/init.rs	run() computes journal_defaults and threads into onboarding or noninteractive_defaults; initialize_project() calls new apply_journal_init() before writing config.
Journal Apply / Outcome crates/tempyr-cli/src/commands/init.rs	Replaces decide_journal_init with apply_journal_init returning JournalInitOutcome { summary_lines }; journal_config_summary now formats [journal] enabled = ... from explicit selection and git context.
Tests & Coverage crates/tempyr-cli/src/commands/init.rs, crates/tempyr-cli/src/commands/onboarding.rs, crates/tempyr-cli/tests/integration.rs	Adds tests for initial index rebuild and journal bootstrap during init; updates onboarding tests for new page ordering and per-option toggles; minor integration test doc and assertion tweaks.

Sequence Diagram

sequenceDiagram
    participant User
    participant Init as init::run()
    participant GitDetect as journal_setup_defaults()
    participant Onboarding as onboarding::run()
    participant Wizard as WizardState
    participant Apply as apply_journal_init()

    User->>Init: Start `tempyr init`
    Init->>GitDetect: Compute JournalSetupDefaults from repo/git visibility
    GitDetect-->>Init: Return defaults
    Init->>Onboarding: Launch wizard (interactive) or noninteractive with defaults
    Onboarding->>Wizard: Initialize pages including JournalSetup with defaults
    User->>Onboarding: Interact (toggle journal options)
    Wizard-->>Onboarding: Return OnboardingSelections
    Onboarding-->>Init: Complete with selections
    Init->>Apply: apply_journal_init(root, selections)
    Apply-->>Init: Return summary lines (refspec/config/bootstrap attempts)
    Init-->>User: Write config + output summary

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Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• feat(journal): [journal] config + init wizard + pack-refs (Phase 2 slice 3/3) #24: Prior work on journal init/config and onboarding wiring that this PR refactors (replaces decide_journal_init with defaults-driven flow).

Poem

A rabbit hops through repo light and dim,
Defaults from Git whisper, "enable the brim."
Toggles clicked, the journal wakes and hums,
Bootstrap, fetch, and index—ready as drums. 🐇📚✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 45.83% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title accurately summarizes the main changes: adding a dedicated journal setup page to the onboarding wizard and making the initial index rebuild (via defaults) explicit in the init command.
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.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/onboarding-index-journal-setup

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@crates/tempyr-cli/src/commands/init.rs`:
- Around line 72-85: The noninteractive_defaults function is hard-coding
bootstrap_journal_layout to false which ignores the computed setting in
JournalSetupDefaults; change the OnboardingSelections construction in
noninteractive_defaults to set bootstrap_journal_layout:
journal_defaults.bootstrap_journal_layout (i.e., propagate the
JournalSetupDefaults.bootstrap_journal_layout value into OnboardingSelections)
so the --no-wizard path respects the previously computed default.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: 019f6bea-8c17-49a2-bd2b-b224e54a5f0d

📥 Commits

Reviewing files that changed from the base of the PR and between ef0d861 and d6e0d6d.

📒 Files selected for processing (2)

• crates/tempyr-cli/src/commands/init.rs
• crates/tempyr-cli/src/commands/onboarding.rs