phenotype-tooling

Consolidated Rust workspace for Phenotype-org developer tooling. It replaces duplicated shell and Python scripts scattered across repos with a focused set of clap-based CLIs aligned to the scripting language hierarchy (Rust default; no new Bash).

Overview

phenotype-tooling centralizes build verification, code-quality checks, documentation validation, release support, and software-bill-of-materials generation into a single Rust workspace. Each crate is independently usable and can be adopted by other Phenotype repos without copying implementation logic.

Crates

Pre-FocalPoint Lift

Crate	Purpose	Replaces
docs-health	Markdown vale/markdownlint + broken-link scanner	phenodocs/.airlock/lint.sh, phenodocs/scripts/check_docs_links.py
fr-trace	FR-NNN -> test traceability scanner	repos/scripts/traceability-check.py (+3 duplicates)
quality-gate	Aggregates cargo fmt/clippy/test pass-fail	30+ duplicated scripts/quality-gate.sh files
legacy-scan	Detects shell/Python anti-patterns per scripting policy	docs/governance/scripting_policy.md rubric

FocalPoint Lift (10 tools from Section 6 of PLAN.md)

Crate	Purpose	Source
agent-orchestrator	Multi-lane agent task dispatcher and state tracker	FocalPoint tooling/agent-orchestrator/
audit-privacy	iOS privacy manifest auditing (scope: Apple plist analysis)	FocalPoint apps/ios/FocalPoint/scripts/audit-privacy/
bench-guard	Benchmark regression detection and thresholds	FocalPoint tooling/bench-guard/
commit-msg-check	Enforces conventional commits + linkage rules	FocalPoint tooling/commit-msg-check/
doc-link-check	Validates markdown links without crawling	FocalPoint tooling/doc-link-check/
fr-coverage	Functional Requirement test coverage analyzer	FocalPoint tooling/fr-coverage/
release-cut	Automated semver release and changelog generation	FocalPoint tooling/release-cut/
sbom-gen	SBOM (CycloneDX/SPDX) generation from Cargo.lock	FocalPoint tooling/sbom-gen/
fuzz-setup	Fuzzing corpus reference and setup templates	FocalPoint fuzz/

Migration plan

1. Scaffold (this repo): clap skeletons emitting stub JSON reports.
2. Port logic: port each source script into its crate, preserving exit codes and expected output; retain the shell script as a thin wrapper calling the Rust binary during the transition.
3. Roll out: replace scripts/quality-gate.sh in each consumer repo with a one-line shim that invokes the released quality-gate binary; then delete the shim once CI is green.
4. Decommission: remove the Python traceability-check.py and check_docs_links.py variants.

Target consumer repos (partial list): AgilePlus, HexaKit, PhenoKits, heliosApp, Civis, PolicyStack, thegent, portage, phenodocs, Pyron, phenoDesign.

Install

Each binary can be installed independently via cargo install:

# Install a single tool
cargo install --path crates/quality-gate

# Or install all tools
for crate in agent-orchestrator bench-guard commit-msg-check doc-link-check fr-coverage release-cut sbom-gen fuzz-setup; do
  cargo install --path crates/$crate
done

# Verify installed
cargo install --list

Adoption in Other Repos

Use the provided scripts/adopt-tooling.sh to symlink phenotype-tooling binaries into any Phenotype repo:

# In your target repo
cd /path/to/my-repo
bash /path/to/phenotype-tooling/scripts/adopt-tooling.sh

# Now you can use tools from tooling/ symlinks
./tooling/quality-gate
./tooling/fr-coverage --help

Build

cargo check --workspace
cargo test --workspace
cargo clippy --workspace -- -D warnings
cargo fmt --check
cargo build --release --workspace

Governance & Worklogs

• CLAUDE.md documents repo-specific conventions and workspace rules.
• AGENTS.md gives AI agents the local routing and quality-gate pointers.
• worklogs/ captures repo-local research, architecture, and governance notes.
• CHANGELOG.md tracks release-visible changes.

License

MIT. See LICENSE.