Add single-record YAML curation skill

.claude/skills/curate-yaml-record/SKILL.md

@@ -0,0 +1,137 @@
+---
+name: curate-yaml-record
+description: Review and curate one CommunityMech community, isolate, or reusable taxon YAML record for ecological scope, taxonomy, interactions, cultivation, environment, claim-level evidence, completeness, and resolvable gaps. Use for a named record audit or improvement; do not use for bulk scouting/ingestion or as permission to contact anyone, spend provider credits, or mutate GitHub.
+allowed-tools: Bash, Read, Grep, Glob, WebSearch, WebFetch, Edit, Write
+metadata:
+  category: curation
+  requires_database: false
+  requires_internet: true
+  version: 1.0.0
+---
+
+# Curate one CommunityMech YAML record
+
+Produce a defensible community or taxon record and an explicit account of what
+is supported, corrected, missing, and genuinely unknown. Search results and raw
+research reports are leads; only inspected sources can support a claim.
+
+## Boundaries
+
+- Resolve one target under `kb/communities/`, `data/isolates/`, or `kb/taxa/`.
+  If a name matches several communities, experiments, or taxon records, stop
+  and disambiguate before editing.
+- An audit/review request is read-only. Curate, improve, complete, correct, or
+  add-evidence requests authorize local edits to the named record and the
+  smallest necessary history/generated-product paths.
+- Do not generalize a strain pair, enrichment, synthetic consortium, or
+  cultivation experiment into a natural-community claim.
+- Never make an external provider call, spend credits, contact authors, or
+  create/edit a GitHub item or other outbound message without explicit
+  authorization for that action.
+- Preserve unrelated work and use a dedicated branch/worktree for multi-file
+  changes.
+- Never fill an optional field merely for coverage or interpret absence as
+  evidence of absence.
+
+## Read before judging the record
+
+Read the full target plus:
+
+- `CLAUDE.md`;
+- the applicable `MicrobialCommunity` or `CommonTaxon` class and the taxonomy,
+  interaction, environment, cultivation, evidence, discussion, and history
+  classes in `src/communitymech/schema/communitymech.yaml`;
+- `history/README.md`;
+- [references/review-checklist.md](references/review-checklist.md).
+
+Inspect reusable `kb/taxa/` records, related communities, committed reference
+cache entries, and any source data named by the record. Rendered pages and raw
+research prose are not independent evidence.
+
+## Workflow
+
+### 1. Establish the baseline
+
+Read the entire YAML. Record its ID, name, category/state/origin, environment,
+taxa, interactions, factors, cultivation/growth media, external resources,
+datasets, discussions, evidence, and curation history. For a community record:
+
+```bash
+just validate <record-path>
+just validate-strict <record-path>
+just validate-terms <record-path>
+just validate-references-explained <record-path>
+```
+
+For `kb/taxa/`, use the dedicated taxon and term gates (`just validate-taxa`
+and `just validate-terms-taxa`). A green schema result proves structure, not
+ecological or evidentiary correctness.
+
+### 2. Verify identity, scope, and taxonomy first
+
+Confirm whether the record represents a natural community, enrichment,
+synthetic consortium, isolate inventory, or another defined scope. Verify every
+NCBITaxon/GTDB identifier, canonical label, strain designation, reusable taxon
+reference, and community membership claim. Preserve source taxonomic names and
+reclassification context instead of silently translating uncertain taxa.
+
+### 3. Review every scientific claim
+
+For each taxon, ecological interaction, environmental condition, metal,
+metabolite, growth medium, cultivation condition, dataset, and causal direction,
+verify that the cited source supports the exact participants, strain/taxon
+scope, setting, direction, and strength of wording.
+
+Every curated assertion should carry evidence at the claim it supports. Confirm
+stable identifiers and exact snippets against committed abstract, full-text,
+or supplement caches. Do not paraphrase a snippet, join non-contiguous text, or
+present a database/search assertion as a primary experiment.
+
+### 4. Assess completeness and resolve supported gaps
+
+Apply the checklist and use bounded searches for consequential gaps. Prioritize:
+
+1. wrong community scope or member identity;
+2. unsupported or reversed interactions and causal edges;
+3. missing strain, experimental, spatial, or environmental context;
+4. cultivation/growth claims linked to the wrong community or medium;
+5. missing evidence on material composition, function, or outcome claims.
+
+Do not add a generic discussion for every empty slot. A discussion should name
+a concrete uncertainty, what was checked, why it matters, and what source would
+resolve it.
+
+### 5. Write through the guarded path
+
+Use a narrowly scoped mutator that loads the record, asserts its ID/path,
+changes only reviewed nodes, calls
+`communitymech.curate.curation_event.record_curation_event` with
+`llm_assisted=True`, and writes through
+`communitymech.validation.write_validated.write_validated_community`.
+For a reusable taxon, pass `target_class="CommonTaxon"`; the default is
+`MicrobialCommunity`.
+
+Use `curator="claude"` when no identity was supplied. Do not attribute agent
+judgement to the user and do not append an event if content is unchanged.
+Create the required append-only repository history entry with `just
+new-history`; never revise an older history record.
+
+### 6. Verify and report
+
+Repeat the focused validation and run proportional wider gates:
+
+```bash
+just validate-history
+just audit-writers
+just qc
+git diff --check
+git diff -- <record-path> history src scripts docs
+```
+
+If a community record changed, regenerate/check committed pages with `just
+gen-html` and `just check-docs-current` as required. Re-read the result and
+ensure citations, snippets, and history describe the actual diff.
+
+Report corrections/additions and sources, retained claims checked, unresolved
+gaps and bounded searches, target class used, history artifact, and validation
+results. CommunityMech has no record-level REVIEWED flag; never invent one.

.claude/skills/curate-yaml-record/references/review-checklist.md

@@ -0,0 +1,32 @@
+# CommunityMech record review checklist
+
+Use this checklist for one `MicrobialCommunity` or `CommonTaxon`; it does not
+require every optional field to be populated.
+
+## Evidence standard
+
+- An `EvidenceItem` needs a stable reference, `supports`, evidence source, and
+  exact source snippet.
+- Evidence belongs on the narrowest taxon, interaction, environment, or other
+  assertion it supports.
+- An association, co-occurrence, or enrichment does not establish ecological
+  interaction direction or causality.
+- A paper about a related strain or community is not evidence for the target
+  without an explicit, justified scope relation.
+- Record negative searches as bounded “not found” results.
+
+## Field-by-field audit
+
+| Area | Verify | Complete enough when |
+|---|---|---|
+| Identity/scope | ID, name, origin, category, ecological state, and experimental/natural scope agree. | The record denotes one clearly bounded community or reusable taxon. |
+| Taxonomy | NCBITaxon/GTDB identity, canonical label, strain, lineage, and reusable-record link agree. | Every member is resolvable or explicitly uncertain without false precision. |
+| Composition | Member inclusion, abundance/role wording, sampling state, and source scope match. | Composition does not combine incompatible time points, sites, or treatments. |
+| Interactions | Source, target, interaction type, direction, scope, participants, and evidence agree. | Co-occurrence is not upgraded to interaction or causation. |
+| Environment | ENVO term/label, modeled setting, parameters, units, and source context agree. | Natural, host-associated, and engineered contexts remain distinct. |
+| Cultivation | Medium, ingredient, vessel, temperature, atmosphere, duration, and measured outcome match. | Conditions are attached to the experiment/community that actually used them. |
+| Metals/metabolites | Identity, role, direction of exchange, and experimental support agree. | Presence is not treated as function and a measured analyte is not a causal actor without evidence. |
+| Causal claims | Nodes exist, edges have the right direction/type, and every edge has evidence. | Mechanistic graphs preserve organism and experimental scope. |
+| Datasets/resources | Identifier resolves and relevance is explicit. | The list is not a bibliography dump. |
+| Discussions | Each item is a concrete unresolved question or conflict. | Checked sources and a resolution condition are named. |
+| Audit | Per-record history and repository history reflect the exact change. | LLM assistance is explicit and prior history remains append-only. |

CLAUDE.md

@@ -132,6 +132,11 @@ corpus has a known evidence-repair backlog (#417). It is not a CI gate.
 
 ## Editing a community or taxon record
 
+Use [curate-yaml-record](.claude/skills/curate-yaml-record/SKILL.md) when the
+request is to audit or improve one named community, isolate, or reusable taxon
+record. It is read-only for review requests and applies the evidence, guarded
+write, and append-only history contracts below.
+
 1. Read the target, schema, and strong neighboring records.
 2. Check whether the same taxon should reference a reusable record in `kb/taxa`.
 3. Make the smallest source-supported change; preserve experimental context and