docs: align documentation to current implementation state#19
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Major documentation updates across the project: - Enhanced CLAUDE.md with detailed CLI usage patterns for new-project and clone-project - Added comprehensive secrets management configuration examples (env, file, vault) - Expanded extension YAML schema documentation with all install methods and BOM fields - Documented three test suite levels (smoke, integration, full) with timing and use cases - Updated GitHub Actions workflow count (9→10) and descriptions Cleanup and maintenance: - Removed deprecated vf-skill-creator extension and related files - Fixed broken cross-references in vf-import-to-ontology docs - Standardized docker-compose→docker compose in examples - Updated GitHub Actions checkout versions (v3→v6) - Corrected extension count (74→70+) in documentation New documentation: - Added GPU.md for GPU configuration guidance - Added MANIFEST.md for manifest schema documentation - Added check-links.yml workflow for link validation - Added agent-manager upgrade script Registry updates: - Updated profiles.yaml and registry.yaml to reflect current extensions - Enhanced manifest.schema.json with additional validation rules 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Trimmed CLAUDE.md from 675 to 171 lines (75% reduction) by: - Removing detailed CLI documentation (→ docs/CLI.md) - Removing extensive architecture details (→ docs/ARCHITECTURE.md) - Removing full extension YAML structure (→ docs/EXTENSION_AUTHORING.md) - Removing detailed testing instructions (→ docs/TESTING.md) - Removing secrets management examples (→ docs/SECRETS_MANAGEMENT.md) CLAUDE.md now provides: - Concise project overview with core principles - Quick command reference for common tasks - High-level architecture concepts - Brief extension development guide - Code standards summary - Important architectural patterns - Comprehensive documentation index Also applied prettier formatting to maintain consistency across documentation files and schemas. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
- Update jira-mcp and linear-mcp BOM source from vendor-specific (atlassian/linear) to 'script' to match schema enum values - Fix broken markdown link in vf-import-to-ontology README to use absolute path instead of relative path for better CI compatibility This resolves CI failures: - Schema validation (2 extensions) - Internal markdown link checker (1 broken link) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
The SKILL.md file in vf-import-to-ontology also had the same broken relative link to vf-web-summary that was causing CI failures. Update to use absolute path for consistency. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Replace custom bash script with lychee-action for more robust and faster markdown link validation. This fixes the bug where multiple links on a single line (like in table cells) were not properly parsed and validated. Key improvements: - Use lychee-action@v2 (Rust-based, much faster) - Use actions/cache@v5 (latest version) - Fix multi-link-per-line parsing bug - Add caching for faster subsequent runs - Include fragment/anchor checking in internal validation - Generate markdown reports uploaded as artifacts - Remove separate anchor check job (now integrated) - Configure external link checker with proper timeouts and retries This resolves CI failures in AI-TOOLKIT.md where multiple extension links in a table cell were incorrectly flagged as broken. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
The --base argument requires either a URL with scheme or an absolute path. Using '.' is invalid and causes the workflow to fail. For checking local file:// scheme links, we don't need --base or --root-dir as lychee resolves paths relative to the markdown files. Error was: error: invalid value '.' for '--base <BASE>': Base must either be a URL (with scheme) or an absolute local path. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Fix broken fragment link in vision-flow README. The anchor should be #extension-profiles not #profiles to match the heading in EXTENSIONS.md. Error from lychee: [ERROR] docs/EXTENSIONS.md#profiles | Cannot find fragment 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
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Node.js: add pnpm overrides for brace-expansion (>=5.0.5, DoS) and yaml (>=2.8.3, stack overflow); fastify already at ^5.8.5. Rust: cargo update resolves rand 0.9.2->0.9.4, 0.10.0->0.10.1 and rustls-webpki 0.103.10->0.103.13 (alerts #16, #17, #18, #19, #20). Dismissed alerts #19/#20 tolerable_risk: 0.101.7 remains locked in via AWS SDK rustls 0.21 compat chain (tracked in issue #144). Also fix clippy::unnecessary_sort_by newly enforced by Rust 1.95. Containers: bump yq 4.52.4->4.52.5, gh 2.87.2/2.88.1->2.89.0 and cosign 3.0.5->3.0.6 in Dockerfiles and workflows to address Go stdlib CVEs (CVE-2026-25679, -27137--27142, CVE-2025-15558, CVE-2026-24051). Toolchain: update Rust 1.94->1.95 in rust-toolchain.toml, Cargo.toml, build-base-image.yml defaults, and WORKFLOW_ARCHITECTURE.md. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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