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.claude/skills/README.md

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+# `.claude/skills`
+
+Claude Code skills for working on and with nf-metro. Skills auto-trigger
+from the descriptions in each `SKILL.md` frontmatter; for the conventions
+each one assumes (local paths, env names, render-preview URL), see the
+preamble at the top of the relevant `SKILL.md`.
+
+## Cohort map
+
+The skills fall into three conceptual groups.
+
+### Pipeline-side
+
+For someone integrating nf-metro into their own Nextflow pipeline repo:
+
+| Skill | When to use |
+|---|---|
+| [`pipeline-metro-diagram`](pipeline-metro-diagram/SKILL.md) | Author the `.mmd` content for a pipeline's metro map: lines, stations, sections, off-track inputs, the render-inspect-edit iteration loop. |
+| [`pipeline-metro-setup`](pipeline-metro-setup/SKILL.md) | Wire the rendered map into the pipeline repo: file layout, render commands, README image swap, CHANGELOG, install-line pinning (released version vs named-branch on a fork). |
+
+### nf-metro-side authoring
+
+For someone changing nf-metro itself:
+
+| Skill | When to use |
+|---|---|
+| [`fix-issue`](fix-issue/SKILL.md) | General end-to-end workflow for a GitHub issue: worktree, environment, implement, test, push, PR. The "skeleton" most other nf-metro authoring tasks build on. |
+| [`nf-metro-layout-fix`](nf-metro-layout-fix/SKILL.md) | Drive code-level fixes to nf-metro layout when a real pipeline render exposes a bug. Savepoint pattern, invariant-test-first-then-fix-then-runtime-validator loop, conditional gating, the "improvement ratchet". |
+| [`nf-metro-gate-triage`](nf-metro-gate-triage/SKILL.md) | Run a routing gate-arm triage slice: give every un-exercised branch in a `layout/routing/` module a verdict (reachable -> fixture, defensive, candidate-dead, or reachable-but-defective -> file a bug). Wraps the methodology in [`docs/dev/routing_gate_triage.md`](../../docs/dev/routing_gate_triage.md). |
+| [`pr-chain-vet`](pr-chain-vet/SKILL.md) | Per-PR vetting on a stacked PR chain: gallery diff vs `main`, classify every changed example, `/simplify` pass, sweep narrative comments, get CI green, post-merge cleanup in the right order. |
+
+### Publishing / CI ops
+
+For keeping the docs site and PR render previews actually reaching the web:
+
+| Skill | When to use |
+|---|---|
+| [`pages-ci-doctor`](pages-ci-doctor/SKILL.md) | Diagnose and un-stick GitHub Pages publishing when a `_pr/<N>/` preview 404s or shows stale content, or the docs site didn't refresh after a merge. Walks the `pr-renders -> pr-render-publish -> branch build` chain, detects the recurring legacy-builder stall, re-triggers it, and verifies live through the CDN-caching gotchas. |
+
+### Visual verification
+
+Opt-in only (`disable-model-invocation: true` — the user must invoke
+explicitly):
+
+| Skill | When to use |
+|---|---|
+| [`render-topologies`](render-topologies/SKILL.md) | Local pixel-diff of all gallery renders between the current branch and `origin/main`. Only needed for pre-push confidence; the CI render preview on the PR is the authoritative review. |
+
+### Docs site
+
+| Skill | When to use |
+|---|---|
+| [`serve-docs`](serve-docs/SKILL.md) | Spin up the Astro / Starlight docs site locally for live preview. Wraps `scripts/serve_docs.sh`, which generates the git-ignored gallery / pipelines / playground content and then starts the dev server. |
+
+## How the skills relate
+
+- `pipeline-metro-diagram`'s "is it mmd or nf-metro?" triage in Step 5
+  hands off to `nf-metro-layout-fix` when the diagnosis is engine-side.
+- `nf-metro-layout-fix` Step 4 hands off to `pr-chain-vet` for the
+  per-PR vetting workflow that ships the resulting chain back to `main`.
+- `pipeline-metro-setup` Stage 2 Case B (named-branch pin on a fork) is
+  the bridge developers use *while* `nf-metro-layout-fix` +
+  `pr-chain-vet` work is in flight.
+- `fix-issue` Step 4 references `render-topologies` for the optional
+  pre-push local diff.
+
+## Conventions
+
+Most skills assume:
+
+- Local nf-metro checkout at `~/projects/nf-metro`
+- Upstream slug `seqeralabs/nf-metro` (issues + PR targets)
+- CI render preview at `seqeralabs.github.io/nf-metro/_pr/<N>/`
+
+If your setup differs, substitute in the commands; the conventions are
+called out at the top of each `SKILL.md` so the substitution points are
+visible.
+
+## Step / Stage nomenclature
+
+Most skills use `## Step N: ...` for numbered procedural sections.
+`pipeline-metro-setup` uses `## Stage N: ...` instead — its four stages
+are deliberately coarser-grained (a pipeline-integration journey, not a
+debugging checklist) and the word choice signals that.