Auto-ignore lifecycle state during init

[lzehrung]

Summary

• automatically add .codegraph/ to the resolved project root .gitignore during codegraph init and codegraph sync --init when the lifecycle manifest is untracked and not already effectively ignored
• add --no-update-gitignore, lifecycle result reporting, and CLI/help/docs updates for tracked, disabled, and non-Git cases
• cover ignore-policy edge cases and lifecycle ordering with focused lifecycle and CLI validation tests

Testing

• rtk npx vitest run tests/lifecycle.test.ts tests/cli-options-validation.test.ts
• rtk npm run test:integration
• rtk npm run check
• manual smoke test in a temporary Git repo: init adds one .codegraph/ rule, .codegraph/manifest.json stays out of git status, repeated init does not duplicate, and uninit leaves the rule in place

[Copilot]

Pull request overview

This PR enhances the lifecycle initialization flow to ensure .codegraph/manifest.json doesn’t show up as untracked noise in Git repos by automatically appending a .codegraph/ ignore rule to the resolved project root’s .gitignore when needed, with an explicit opt-out.

Changes:

• Add Git ignore preparation during codegraph init and codegraph sync --init, plus a --no-update-gitignore opt-out and user-facing reporting.
• Introduce Git helpers for “tracked” and “ignored” path predicates and centralize Git error formatting.
• Add focused lifecycle/CLI validation tests and update CLI/help/docs/skill docs to reflect the new behavior and result schema.

Reviewed changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/lifecycle.test.ts	Adds comprehensive Git ignore-policy behavioral tests and CLI output assertions for init/sync --init.
tests/cli-options-validation.test.ts	Validates --no-update-gitignore is only accepted for init and sync --init.
src/util/git.ts	Adds isGitPathTracked/isGitPathIgnored predicates and consolidates Git error creation.
src/lifecycle/manifest.ts	Wires ignore preparation into init and initializing sync; extends sync result with optional gitignore.
src/lifecycle/gitignore.ts	Implements .gitignore update logic (effective-ignore check + safe append + actionable errors).
src/lifecycle/errors.ts	Moves CodegraphLifecycleUserError into a dedicated module and re-exports it.
src/cli/options.ts	Adds --no-update-gitignore to schemas and enforces sync requires --init when using it.
src/cli/lifecycle.ts	Passes updateGitignore through and prints user-facing messages for added/tracked outcomes.
src/cli/help.ts	Updates lifecycle help text to document ignore-policy behavior and opt-out flag.
docs/cli.md	Documents ignore semantics, new flag, and JSON schema additions for initializing commands.
codegraph-skill/codegraph/SKILL.md	Updates skill docs/examples to include ignore-policy behavior and --no-update-gitignore.
.gitignore	Ignores .codegraph/ in this repo.

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[kilo-code-bot]

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (12 files)

• .gitignore
• codegraph-skill/codegraph/SKILL.md
• docs/cli.md
• src/cli/help.ts
• src/cli/lifecycle.ts
• src/cli/options.ts
• src/lifecycle/errors.ts
• src/lifecycle/gitignore.ts
• src/lifecycle/manifest.ts
• src/util/git.ts
• tests/cli-options-validation.test.ts
• tests/lifecycle.test.ts

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_{Reviewed by kimi-k2.6-20260420 · Input: 310.7K · Output: 26.6K · Cached: 343.6K}