Converge note-frontmatter contract to one shared zod schema

.claude/commands/iwc-survey-pattern.md

@@ -13,7 +13,7 @@ Write or refine exactly one pattern page under `content/patterns/` from a survey
 2. **`CLAUDE.md`** — local authoring rules.
 3. **`docs/PATTERNS.md`** — operation-anchored naming, corpus-first rule, legacy-tool posture.
 4. **`docs/ARCHITECTURE.md`** §3, §5, §6 — note types, frontmatter, validation.
-5. **`meta_schema.yml`** + **`meta_tags.yml`** — frontmatter contract and tags.
+5. **`packages/note-schema/src/note-schema.ts`** + **`meta_tags.yml`** — frontmatter contract and tags.
 6. **`common_paths.yml.sample`** — citation prefix vocabulary; use `$IWC_FORMAT2/path:line` citations.
 7. **The survey at `$1`** — especially the candidate boundary, decisions, and open-question resolution relevant to `$2`.
 
@@ -55,7 +55,7 @@ Drop sections that do not earn their space. A thin “None surfaced” legacy se
 
 ## Frontmatter guidance
 
-- Required fields must conform to `meta_schema.yml`; do not add ad-hoc fields.
+- Required fields must conform to the `@galaxy-foundry/note-schema` contract; do not add ad-hoc fields.
 - Set `pattern_kind: operation` for concrete operation pages, `pattern_kind: recipe` for multi-step lifecycle pages, and `pattern_kind: moc` for map-of-content pages that route readers to operations and recipes.
 - `summary` is a compressed “what to do and when” line, not a mini abstract.
 - `related_notes` should name primary source notes only, usually the survey. Put secondary context notes in body or `See also` unless they are essential source material.

.claude/commands/iwc-survey.md

@@ -13,7 +13,7 @@ Produce or refresh `content/research/iwc-$1-survey.md`. The survey **proposes ca
 2. **`CLAUDE.md`** — authoring rules.
 3. **`docs/PATTERNS.md`** — pattern-authorship policy. **Operation-anchored naming** is mandatory in candidate-pattern proposals; do not surface tool-anchored names. Corpus-first applies — no speculative candidates.
 4. **`docs/ARCHITECTURE.md`** §3 (note types), §5 (frontmatter), §6 (validation).
-5. **`meta_schema.yml`** + **`meta_tags.yml`**.
+5. **`packages/note-schema/src/note-schema.ts`** + **`meta_tags.yml`**.
 6. **`common_paths.yml.sample`** — `$IWC_FORMAT2` is the cleaned `gxformat2` corpus root for grep work and full-workflow reads; `$IWC_SKELETONS` mirrors that tree with non-structural fields stripped (tool_ids + topology + control flow only) — cheap structural scans for step-pair / step-sequence patterns; `$IWC` is the upstream `.ga` source for permalinks. Write citations as `` `$IWC_FORMAT2/path:line` `` (or `` `$IWC_SKELETONS/path:line` `` when the structural view is what's evidenced).
 7. **`content/research/iwc-shortcuts-anti-patterns.md`** — already-pinned "don't endorse" calls. Do not re-surface anything covered here as a recommendation.
 8. **Existing surveys** under `content/research/iwc-*-survey.md` — for shape and tone, and to detect topic overlap.

.claude/commands/review-mold.md

@@ -29,7 +29,7 @@ Run it once and trust it. Do **not** re-derive these checks by hand — spend to
 2. **`CLAUDE.md`** / **`AGENTS.md`** — authoring rules.
 3. **`docs/MOLD_SPEC.md`** — Mold source layout and the eval/usage/refinement contract; reference-kind taxonomy; `load`/`mode`/`used_at` semantics.
 4. **`docs/COMPILATION_PIPELINE.md`** — what Cast does with each reference kind; `mode: verbatim` vs LLM-condensed.
-5. **`meta_schema.yml`** — only the Mold-specific shapes (`references[]` schema). Skim, don't memorize.
+5. **`packages/note-schema/src/note-schema.ts`** — only the Mold-specific shapes (`references[]` schema). Skim, don't memorize.
 6. **`common_paths.yml.sample`** — citation-prefix vocabulary for resolving inline `$NAME/...` corpus references.
 7. **The Mold itself** — `content/molds/$1/`:
    - `index.md` (frontmatter + body)

.claude/commands/review-pattern.md

@@ -12,7 +12,7 @@ Review the note at `$1` and return a structured report. Do **not** edit files 
 1. **`content/glossary.md`** — pinned vocabulary (Mold, Pipeline, Pattern, Cast, axis, …). Misreading these terms breaks the review.
 2. **`CLAUDE.md`** — authoring rules (`additionalProperties: false`, registered tags, wiki-link conventions, "don't weaken the schema").
 3. **`docs/ARCHITECTURE.md`** §3 (note types), §5 (frontmatter contract), §6 (validation pipeline). Skim the rest only if needed.
-4. **`meta_schema.yml`** + **`meta_tags.yml`** — frontmatter and tag enums.
+4. **`packages/note-schema/src/note-schema.ts`** + **`meta_tags.yml`** — frontmatter and tag enums.
 5. **`common_paths.yml.sample`** — the citation prefix vocabulary. Logical names (`$IWC`, `$IWC_FORMAT2`, `$GALAXY`, `$TOOLS_IUC`, `$PLANEMO`, `$GXFORMAT2`) map to filesystem paths and (when set) GitHub repos. Resolve every `$NAME/...` citation in the note via this file before checking it.
 6. **The note's `related_notes` and survey/research companions** — pinned decisions live in `## Decisions` sections (e.g. `iwc-tabular-operations-survey.md` §7). Treat those as binding unless the review surfaces a reason they're wrong; if so, flag for both the note *and* the source decision record.
 
@@ -32,7 +32,7 @@ For research notes:
 
 1. **Correctness vs tool source** — anything the wrapper contradicts is a fix-before-merge.
 2. **Correctness vs corpus** — citations resolve, ranges are tight, paraphrases are faithful.
-3. **Schema / tag conformance** — frontmatter validates against `meta_schema.yml`, all tags appear in `meta_tags.yml`. Note: `additionalProperties: false`, so unknown frontmatter fields are blockers.
+3. **Schema / tag conformance** — frontmatter validates against the `@galaxy-foundry/note-schema` contract, all tags appear in `meta_tags.yml`. Note: per-type members are `.strict()`, so unknown frontmatter fields are blockers.
 4. **Survey decision conformance** — `## Decisions` sections in companion research notes are binding. Drift between page and decision record is a flag on both.
 5. **Form quality for casting** — pattern pages get LLM-condensed into cast skills; reference content should be "do this," not "what we considered." Pitfalls concrete; wiki-links meaningful.
 

.github/workflows/deploy.yml

@@ -11,9 +11,29 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: withastro/action@v3
+
+      - uses: actions/setup-node@v4
         with:
-          path: site
+          node-version: 20
+
+      - name: Enable corepack
+        run: corepack enable
+
+      # site is a pnpm workspace member; its @galaxy-foundry/* deps resolve to
+      # sibling packages that must be built to dist before Astro imports them.
+      - name: Install dependencies
+        run: pnpm install --frozen-lockfile
+
+      - name: Build packages
+        run: npm run packages-build
+
+      - name: Build site
+        run: npm run site:build
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site/dist
   deploy:
     needs: build
     runs-on: ubuntu-latest

.github/workflows/packages.yml

@@ -36,9 +36,6 @@ jobs:
       - name: Validate content
         run: npm run validate
 
-      - name: Install site dependencies
-        run: npm --prefix site install --no-audit --no-fund
-
       - name: Typecheck root and site
         run: npm run typecheck
 

AGENTS.md

@@ -16,7 +16,7 @@
 
 ## Authoring rules
 
-- **Frontmatter is contract.** `meta_schema.yml` is JSON Schema Draft 07 with `additionalProperties: false`. Unknown fields are rejected. Add a property declaration in the schema before adding a frontmatter field anywhere.
+- **Frontmatter is contract.** The single source of truth is the zod schema in `@galaxy-foundry/note-schema` (`buildNoteSchema`, `packages/note-schema/src/note-schema.ts`), shared by the validator and the Astro site — there is no separate JSON-Schema mirror. Per-type members are `.strict()`, so unknown fields are rejected. Add a field to the relevant member before using it in frontmatter anywhere.
 - **Tags must be registered.** Every tag a note uses lives in `meta_tags.yml`. Vocabulary changes touch one file.
 - **Wiki-link fields use `[[Target]]`.** Single-value fields (`parent_pattern`) and array fields (`related_notes`, `related_patterns`, `related_molds`, `patterns`, `cli_commands`, `prompts`).
 - **Polished IWC references should survive corpus churn.** Pattern pages, Mold pages, and other polished content should cite abstract IWC workflow IDs without generated extensions or fixture roots, e.g. `transcriptomics/rnaseq-pe/rnaseq-pe`, plus step labels or step IDs when needed. Do not cite generated `.ga`/`.gxwf.yml` paths or line numbers in polished pages; reserve those for surveys, ad-hoc research notes, and local debugging evidence.

README.md

@@ -38,7 +38,7 @@ Two flows feed the Foundry:
 
 Casting produces skill artifacts: `npm run cast -- --mold=<slug> --target=<target>`.
 
-Frontmatter is contract-enforced by `meta_schema.yml`; every note carries a registered tag from `meta_tags.yml`. Validate before commit.
+Frontmatter is contract-enforced by the shared zod schema in `@galaxy-foundry/note-schema` (used by both the validator and the site); every note carries a registered tag from `meta_tags.yml`. Validate before commit.
 
 ## Tooling
 

content/glossary.md

@@ -82,7 +82,7 @@ Alphabetical.
 
 **Scenario note** — Mold- or Pipeline-owned content (`scenarios.md`): the **concrete test cases** the eval oracle is applied against (a Mold input, or a whole-journey input for a Pipeline). Each case binds a fixture/input and states its expected values or assertions as free text (e.g. "CalliNGS-NF → 11 processes from root `modules.nf`", "`sort([3,1,2]) == [1,2,3]`"). All fixture-specific concreteness lives here, keeping the **Evaluation plan** (`eval.md`) a pure abstract oracle. A **run** pairs a scenario's output with the eval oracle's property checks (driven by `/test-drive`). Foundry-maintainer infrastructure; never packaged into cast artifacts. Distinct from **Evaluation plan** (abstract checker), **Usage note** (illustration), and **Refinement note** (design questions).
 
-**Schema (Mold IO)** — a JSON Schema file declaring the input or output shape of a Mold (e.g., the per-source summary schemas, the Galaxy tool summary schema). Lives in `schemas/` (a non-content directory; not a vault note). Referenced by Molds via typed-path frontmatter fields; copied verbatim into cast bundles by casting. Distinct from `meta_schema.yml`, which is the *frontmatter* contract for content notes.
+**Schema (Mold IO)** — a JSON Schema file declaring the input or output shape of a Mold (e.g., the per-source summary schemas, the Galaxy tool summary schema). Lives in `schemas/` (a non-content directory; not a vault note). Referenced by Molds via typed-path frontmatter fields; copied verbatim into cast bundles by casting. Distinct from the *frontmatter* contract for content notes, which is the shared zod schema in `@galaxy-foundry/note-schema`.
 
 **Subway map** — informal name for the visual rendering of a Pipeline as a vertical line of stops: Mold-shaped phases are linked stations, `[loop]` decorates per-step stations, `[branch]` stops are decision diamonds with their inner branches/chains expanded, future `[gate]` stops would render as checkpoint markers. Off-ramps per stop point to the patterns / CLI manpages / schemas the Mold references — the reference-surface drill-downs from a journey-surface point. Rendered by `[...slug].astro` via `PipelineBody.astro` + `PhaseGraph.astro`; the per-pipeline harness off-ramp lives at `pipelines/[slug]/harness.astro`.