docs: promote Integrity Filtering as primary, restructure GitHub Tools reference pages

[dsyme]

Summary

Promotes Integrity Filtering () as the primary security feature for content filtering, replacing GitHub Lockdown Mode throughout the docs. Also restructures the GitHub Tools reference pages by splitting out checkout and cross-repository content into dedicated pages.

Changes

Integrity Filtering promotion

• Security Architecture (): Replaces the "GitHub Lockdown Mode" section with "Integrity Filtering", updates the security layers table and related links
• Lockdown Mode (reference/lockdown-mode.md): Replaced with a deprecation notice and migration guide (lockdown: true → min-integrity: approved, lockdown: false → min-integrity: none)
• Integrity Filtering (reference/integrity.md): Fixes title/typo, adds Write-Sink Auto-Derivation section (moved from github-tools), removes stale lockdown cross-links
• FAQ (reference/faq.md): Replaces "What is lockdown mode" Q&A with "How does integrity filtering protect my workflow"
• Glossary (reference/glossary.md): Replaces Lockdown Mode entry with Integrity Filtering; updates XPIA cross-reference
• Common Issues (troubleshooting/common-issues.md): Renames "GitHub Lockdown Mode Blocking Expected Content" → "Integrity Filtering Blocking Expected Content", updates guidance to use min-integrity
• GitHub Tools (reference/github-tools.md): Replaces Lockdown Mode section with Integrity Filtering summary; removes duplicate integrity level table
• frontmatter-full.md: Marks lockdown: field as deprecated
• auth.mdx: Removes lockdown mode from additional-auth requirements list
• Blog posts (2026-01-13, 2026-01-24, 2026-01-27): Updates all lockdown-mode references to use integrity filtering language

New reference pages

• reference/checkout.md (new): Full checkout: frontmatter reference — disabling checkout, configuration options table, fetching additional refs, checkout merging, current: true
• Cross-Repository (reference/cross-repository.md): Replaces the long checkout section with a short summary linking to the new page; enriches the GitHub Tools reading section

TOC updates (astro.config.mjs)

• Added: Integrity Filtering, GitHub (Checkout), APM Dependencies, Playwright
• Replaced: "GitHub Lockdown Mode" → "Integrity Filtering"

[Copilot]

Pull request overview

Updates the documentation set to make Integrity Filtering (min-integrity) the primary GitHub content filtering mechanism (deprecating “Lockdown Mode”), and restructures GitHub reference docs by splitting checkout and cross-repo content into dedicated pages.

Changes:

• Replace “GitHub Lockdown Mode” guidance throughout docs with Integrity Filtering concepts, links, and configuration examples.
• Deprecate tools.github.lockdown in reference docs and provide migration mappings to tools.github.min-integrity.
• Split GitHub reference material into clearer pages (new Checkout page; cross-repo page trimmed and linked; sidebar reorganized).

Reviewed changes

Copilot reviewed 25 out of 25 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
docs/src/content/docs/troubleshooting/common-issues.md	Renames troubleshooting guidance from Lockdown Mode to Integrity Filtering and updates examples to min-integrity.
docs/src/content/docs/setup/cli.md	Removes/updates CLI option references and updates “pre-agent failures” wording to integrity filtering.
docs/src/content/docs/reference/permissions.md	Retitles/reframes permissions as “GitHub (Read Permissions)” and streamlines guidance.
docs/src/content/docs/reference/lockdown-mode.md	Converts Lockdown Mode page into deprecation + migration guide pointing to Integrity Filtering.
docs/src/content/docs/reference/integrity.md	Promotes Integrity Filtering as primary and removes Lockdown cross-links/relationship section.
docs/src/content/docs/reference/glossary.md	Replaces Lockdown Mode glossary entry with Integrity Filtering and prunes some glossary entries.
docs/src/content/docs/reference/github-tools.md	Reorients GitHub tools page toward reading, integrity filtering, repo restrictions, cross-repo reading, remote mode, and auth.
docs/src/content/docs/reference/frontmatter-full.md	Marks lockdown: as deprecated and updates guard-policy comment wording.
docs/src/content/docs/reference/faq.md	Replaces lockdown FAQ entry with integrity filtering explanation and updates checkout-related link target.
docs/src/content/docs/reference/dependabot.md	Retitles Dependabot reference page.
docs/src/content/docs/reference/cross-repository.md	Shortens cross-repo page and links out to the new checkout reference; updates cross-repo reading section.
docs/src/content/docs/reference/checkout.md	Adds a dedicated checkout reference page (disable checkout, options table, fetch refs, merging, current: true).
docs/src/content/docs/reference/auth.mdx	Removes lockdown mode from additional-auth requirements list.
docs/src/content/docs/patterns/trial-ops.md	Streamlines TrialOps pattern doc and removes some warnings/tips/sections.
docs/src/content/docs/patterns/multi-repo-ops.md	Updates cross-repo reading link target.
docs/src/content/docs/introduction/architecture.mdx	Replaces Lockdown Mode architecture section with Integrity Filtering and updates security layers table.
docs/src/content/docs/guides/getting-started-mcp.md	Updates remote/local mode anchor link to match new GitHub tools page structure.
docs/src/content/docs/blog/2026-01-27-operational-patterns.md	Updates public-repo triage guidance from lockdown disablement to min-integrity configuration.
docs/src/content/docs/blog/2026-01-24-design-patterns.md	Updates public-repo triage guidance to min-integrity: none with Integrity Filtering link.
docs/src/content/docs/blog/2026-01-13-meet-the-workflows.md	Updates issue triage guidance from lockdown: false to min-integrity: none.
docs/src/content/docs/agent-factory-status.mdx	Adds a workflow entry and updates the engine label for “Grumpy Code Reviewer”.
docs/slides/index.md	Updates slide terminology from “GitHub Guard” to “Integrity”.
docs/interactive-run-mode.md	Removes --auto-merge-prs from interactive mode flag list.
docs/astro.config.mjs	Reorganizes reference TOC/sidebar to add new GitHub sub-pages and Integrity Filtering entry.
.github/workflows/glossary-maintainer.md	Tightens glossary maintainer instructions for where to look for new terminology.

Comments suppressed due to low confidence (2)

docs/src/content/docs/reference/github-tools.md:25

• In the toolset list, this page states that the default toolsets include users, but the MCP guide (e.g., docs/src/content/docs/guides/getting-started-mcp.md:100) explicitly notes that users is not included by default with Actions tokens. Please align this page’s Default list with the actual [default] expansion (i.e., exclude users, or clarify that it depends on token type).

**Available**: `context`, `repos`, `issues`, `pull_requests`, `users`, `actions`, `code_security`, `discussions`, `labels`, `notifications`, `orgs`, `projects`, `gists`, `search`, `dependabot`, `experiments`, `secret_protection`, `security_advisories`, `stargazers`
**Default**: `context`, `repos`, `issues`, `pull_requests`, `users`

docs/src/content/docs/reference/github-tools.md:37

• Typo: “requuire” → “require”.

Some toolsets requuire [additional authentication](#additional-authentication-for-github-tools).

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