supply-chain-ecosystem-quirks

name	supply-chain-ecosystem-quirks
description	Ecosystem-specific supply-chain gotchas for npm, PyPI, conda/pixi, cargo, and Go. Use when reviewing package.json + .npmrc, pyproject.toml + setup.py, pixi.toml + conda-lock.yml, Cargo.toml + .cargo/config.toml, or go.mod + GOPROXY config — any time a supply-chain recommendation depends on which ecosystem you're in. Loads ecosystem-specific reference docs on demand.
metadata	{"references":["references/npm-quirks.md","references/pypi-quirks.md","references/conda-pixi-quirks.md","references/cargo-go-quirks.md"]}

Supply Chain Ecosystem Quirks

Threat Model

Each package manager has unique install-time execution vectors and config knobs that decide whether the general patterns from supply-chain-dependency-security and supply-chain-hardened-ci-cd actually hold. Escape hatches that need explicit auditing per ecosystem: npm postinstall, Python .pth and setup.py, unsigned conda channels, Cargo build.rs, GOSUMDB=off.

Ecosystem Detection and References

Trigger files identify which ecosystem is in scope; each row lists the reference doc to load for the full checklist. Run the bash one-liner to auto-detect, or scan the trigger column manually.

Ecosystem	Trigger files	Reference
npm / yarn / pnpm	package.json, .npmrc, package-lock.json, yarn.lock, pnpm-lock.yaml	references/npm-quirks.md
PyPI / pip / uv / poetry	pyproject.toml, setup.py, requirements.txt, uv.lock, poetry.lock	references/pypi-quirks.md
conda / pixi	pixi.toml, pixi.lock, environment.yml, conda-lock.yml, .condarc	references/conda-pixi-quirks.md
cargo	Cargo.toml, Cargo.lock, .cargo/config.toml	references/cargo-go-quirks.md
Go	go.mod, go.sum, GOPROXY env	references/cargo-go-quirks.md

# Auto-detect: prints one line per ecosystem present, naming the reference doc to load
test -f package.json && echo "npm -> references/npm-quirks.md"
{ test -f pyproject.toml -o -f setup.py -o -f requirements.txt; } && echo "PyPI -> references/pypi-quirks.md"
{ test -f pixi.toml -o -f environment.yml -o -f conda-lock.yml; } && echo "conda -> references/conda-pixi-quirks.md"
test -f Cargo.toml && echo "cargo -> references/cargo-go-quirks.md"
test -f go.mod && echo "Go -> references/cargo-go-quirks.md"

If nothing prints, the project has no packaging-manifest layer this skill covers — return the no-op report (bottom of file).

Quick-Check Battery

Run this block from the project root. Each line either prints nothing (PASS) or emits a FAIL: / WARN: line you can grep FAIL: on. Skip ecosystems not present.

# npm — install-time scripts, lockfile, CI command discipline
grep -q 'ignore-scripts=true' .npmrc 2>/dev/null || echo "npm FAIL: set ignore-scripts=true in .npmrc"
test ! -f package.json || test -f package-lock.json || echo "npm FAIL: package-lock.json not committed"
grep -rE 'npm (install|ci)' .github/workflows/ 2>/dev/null | grep -v 'npm ci' && echo "npm FAIL: CI must use 'npm ci'"

# PyPI — .pth code execution, PEP 517 isolation, custom build backend
find $(python -c 'import site;print(site.getsitepackages()[0])' 2>/dev/null) -name '*.pth' -exec grep -lE '^(import|exec|os\.|subprocess)' {} \; 2>/dev/null | sed 's/^/pypi FAIL: code-executing .pth: /'
grep -rE 'no-build-isolation' .github/workflows/ Makefile *.sh 2>/dev/null && echo "pypi FAIL: --no-build-isolation removes PEP 517 isolation"
grep -E '^backend-path' pyproject.toml 2>/dev/null && echo "pypi WARN: custom backend-path — audit build backend code"

# conda/pixi — channel discipline, escape hatches
grep -A 5 '^channels:' .condarc pixi.toml 2>/dev/null | grep -q 'defaults' && echo "conda WARN: 'defaults' channel present; prefer conda-forge"
grep -rE '(--no-deps|--no-pin|--force-reinstall)' .github/workflows/ Makefile *.sh 2>/dev/null && echo "conda FAIL: lockfile escape hatch in CI"

# cargo — build.rs surface, --locked discipline
find . -name 'build.rs' -not -path './target/*' 2>/dev/null | head -5 | sed 's/^/cargo INFO: build.rs present: /'
grep -rE  .github/workflows/ 2>/dev/null | grep -v --  &&  


go  GOSUMDB 2>/dev/null | grep -qE  &&  
grep -rE  .github/workflows/ 2>/dev/null | grep -v  &&  

Each printed line maps to one row in the report. For each FAIL, load the matching reference for full remediation guidance.

Application Workflow

Run the four steps below in order. Each step is independently re-runnable.

Step 1 — Detect ecosystems present

Run the auto-detect bash one-liner under ## Ecosystem Detection and References. Record the printed reference paths — these are the only references to load.

Step 2 — Run the quick-check battery

Run the ## Quick-Check Battery block. Pipe to tee quick-check.out; every FAIL: line is a P1 finding handled in step 3, every WARN: is a P2.

Step 3 — Load the matching reference for each FAIL or deep review

For each ecosystem flagged in step 2, or any ecosystem the user asked for a detailed review of, open references/<eco>-quirks.md. Each reference document follows the same shape: a threat-relevance paragraph plus 5-6 sectioned checks, each with a verifying command you can copy-paste. Map each section to PASS/WARN/FAIL using the section's verifying command.

Step 4 — Cross-reference findings against general patterns

Compare each finding to the equivalent control in supply-chain-dependency-security (lockfiles, pinning, scanning) and supply-chain-hardened-ci-cd (OIDC, ephemeral runners, secret hygiene). If an ecosystem quirk conflicts with general guidance — for example, pnpm's strict isolation makes the general "vendor dependencies" guidance unnecessary — the ecosystem-specific quirk wins for that ecosystem. Note the conflict in the report.

Output: Ecosystem Quirks Report

Every PASS/WARN/FAIL must cite a file:line (or absent). Every remediation must name a concrete command, skill, or config knob.

## Ecosystem Quirks Posture: <project>

### Ecosystems Detected
| Ecosystem | Evidence (trigger file path) | Reference loaded |
|-----------|------------------------------|------------------|

### Per-Ecosystem Findings
For each detected ecosystem:

#### <ecosystem>
| Quirk / control | PASS/WARN/FAIL | Evidence (file:line) | Remediation (command or skill) |
|-----------------|----------------|----------------------|-------------------------------|

### Cross-Ecosystem Conflicts with General Patterns
Cite any place an ecosystem quirk overrides `supply-chain-dependency-security` or `supply-chain-hardened-ci-cd`.

### Top Priority Actions
1. <highest-impact runnable remediation>
2. <second>
3. <third>

If no ecosystems detected: return No supported package-manager manifests found; this skill does not apply.