opencode-bioresearcher 1.9.0 → 1.11.0

package/skills/bioresearcher-deep-research/references/citations.md

@@ -1,24 +1,40 @@
 # Citation Formats
 
-Numbered-citation formats per source type, with URL forms.
+Semantic cite-key markers in authored text; numbered citations and the
+bibliography are GENERATED by `evidence-ledger.py render`, never hand-written.
 
 ## Overview
 
-All findings are cited with numbered in-text markers ([1], [2, 3], [1-5]),
-numbered by order of appearance, resolved against a bibliography at the end
-of the document. Each source type has a fixed format so reports stay
-consistent across workers and aspects.
+All authored text (aspect reports, `final_report.draft.md`) cites sources with
+semantic cite-key markers that resolve against the evidence ledger. `render`
+assigns numbers by order of first appearance, rewrites the markers into
+numbered form, and generates the References section from the merged ledger -
+so citation numbers and bibliography entries are never transcribed by hand.
 
-## In-text citation forms
+## Cite-key marker grammar
 
 ```markdown
-Single:    BRAF V600E occurs in ~50% of cutaneous melanomas [1].
-Multiple:  Several studies confirm the association [1, 2, 3].
-Range:     Extensively documented [1-5].
-Timeline:  Approved in 2011 [1] and became standard of care [2, 3].
+Single:    BRAF V600E occurs in ~50% of cutaneous melanomas [@pmid:21639808].
+Multiple:  Several studies confirm the association [@pmid:21639808; @nct:NCT04280705].
 ```
 
-## Bibliography formats by source type
+- Marker: `[@ns:value]`; group members separated by `;` (leading `@` per
+  token optional). `render` rewrites groups as `[1]`, `[2, 3]`, `[1-5]`.
+- Keys are the ledger's derived canonical keys (the `add` banner echoes
+  them): `pmid:` > `doi:` > `pmcid:` for articles, `nct:` for trials,
+  `patent:`, `gene:`, `clinvar:`, `chembl:`/`chebi:`/`unii:` for drugs,
+  ontology ids for diseases, accessions/PDB for datasets (`geo:`, `sra:`, `gb:`, `pdb:`),
+  `url:`/`title:` for web/other. A `doi:`/`pmcid:` marker whose record was promoted to a `pmid:`
+  key by merge still resolves.
+- A bracket whose tokens are not namespace+shape-valid cite-keys (prose like
+  `[@home]`, pandoc-style `[@Chapman2011]`) is left verbatim.
+- Unresolved keys fail `render` (exit 1, no output written) with did-you-mean
+  suggestions - fix the draft or ledger, never hand-number.
+
+## Bibliography formats (renderer output)
+
+The formats below document what `render` (and `bib`) emits per source type;
+`final_report.md`'s References section is generated, not composed.
 
 ### Journal articles (from article_search / article_get)
 
@@ -34,9 +50,9 @@ Example:
 
 When PMID is unavailable, use DOI: `DOI: 10.xxxx/xxxxx`. Both may be given.
 Online ahead of print records legitimately carry no Volume(Issue):Pages - not
-even NCBI has them until assigned; render them locator-less
+even NCBI has them until assigned; they render locator-less
 (`Journal. Year. DOI: .... PMID: ....`). Locator fields are backfilled once
-NCBI assigns them (Step 5a `evidence-ledger.py verify`; the Step 5b
+NCBI assigns them (Step 5a `evidence-ledger.py verify`; the Step 5c
 `vet-references.py` run is the final safety net).
 
 ### Clinical trials (from trial_search / trial_get)
@@ -120,9 +136,10 @@ Example:
 [7] Cutaneous melanoma. MONDO:0002025. https://monarchinitiative.org/MONDO:0002025
 ```
 
-### Datasets / sequences (geo_get / sra_get / genbank_get)
+### Datasets / structures / sequences (pdb / geo_get / sra_get / genbank_get)
 
 ```
+[N] PDB structure [PDB_ID]: [title]. [[method]] Resolution: [res]. https://www.rcsb.org/structure/[PDB_ID]
 [N] GEO series GSEXXXXXX: [title]. [organism]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSEXXXXXX
 [N] SRA run SRRXXXXXXX: [experiment description]. https://trace.ncbi.nlm.nih.gov/Traces/?run=SRRXXXXXXX
 [N] GenBank accession XXXXXXXX.X: [definition]. https://www.ncbi.nlm.nih.gov/nuccore/XXXXXXXX.X
@@ -139,7 +156,7 @@ Example:
 | Source type | Cite? |
 |-------------|-------|
 | Tool-returned articles, trials, patents, annotations | Yes |
-| Statistical/quantitative claims | Yes - always |
+| Statistical/quantitative claims | Yes - always (keyed at capture time) |
 | Direct quotes | Yes |
 | General textbook knowledge ("DNA has 4 bases") | No |
 
@@ -149,13 +166,12 @@ Example:
    NCT ID, or accession.
 2. Cite primary sources over reviews when both are available.
 3. Quote accurately; do not overstate findings beyond what the source says.
-4. Per-aspect files keep their own [1..N]; the orchestrator re-numbers all
-   citations into one bibliography for final_report.md.
+4. Cite-key markers must resolve to ledger records; the worker-side
+   `check --markers` gate catches unresolvable markers before the aspect is
+   reported complete, and `render` fails loudly on any key that still
+   does not.
 5. Access dates only for web sources (tools log their own query date).
-6. Ledger-first: bibliography entries are COPIED from evidence-ledger
-   records (`evidence/<ASPECT>.jsonl`, merged at Step 5a into
-   `evidence/sources.jsonl`). Titles are verbatim; locator fields come only
-   from ledger data (tool output or NCBI-verified backfill). No bibliography
-   entry may contain any field absent from the ledger - if a field is
-   missing, render the ledger's `[MISSING field: ...]` marker rather than
-   composing one from memory.
+6. References are generated by `render` from the merged ledger - never
+   hand-composed, hand-numbered, or copy-pasted. If a ledger field is
+   missing, enrich the record (or let `verify` backfill it) rather than
+   editing rendered output.

package/skills/bioresearcher-deep-research/references/clinical-trials.md

@@ -15,7 +15,7 @@ intervention, or keyword with status/phase filters and CURSOR pagination.
 | Parameter | Type | Notes |
 |-----------|------|-------|
 | query | string (required) | Condition, intervention, or keyword |
-| status | string, optional | e.g. "Recruiting", "Completed" |
+| status | string, optional | single CT.gov v2 enum value, any letter case (uppercased upstream): `Recruiting`, `Active_not_recruiting`, `Not_yet_recruiting`, `Enrolling_by_invitation`, `Completed`, `Suspended`, `Terminated`, `Withdrawn`, `Withheld`, `Unknown`. Commas AND spaces FAIL with HTTP 400 (`"Active, not recruiting"` is rejected) - use the underscore spelling; on 400, drop the filter and triage locally by the returned `status` field |
 | phase | string, optional | e.g. "Phase 1", "Phase 2" |
 | intervention_type | string, optional | e.g. "Drug", "Device" |
 | limit | int 1-50, default 10 | Maximum results per page |

package/skills/bioresearcher-deep-research/references/ensembl-pdb.md

@@ -132,3 +132,5 @@ Structure workflow:
   the workspace matters.
 - Chain ensembl_lookup -> gene_get for human annotation; ensembl_region ->
   variant_get for variant detail; pdb citation sections -> article_get.
+  Never copy `summary.title` (structure title) or `summary.authors` (depositors)
+  into `article` records; deposition titles and authors belong to the coordinate entry.

package/skills/bioresearcher-deep-research/references/report-template.md

@@ -45,7 +45,8 @@ Key findings:
 [Generalizability: where findings apply and where they may not]
 
   ## References
-[Numbered bibliography in references/citations.md format, ordered by first appearance]
+[GENERATED by render from the merged ledger - numbered by first appearance;
+authored drafts end before this section]
 ```
 
 ## Per-aspect file structure (lighter)
@@ -56,25 +57,25 @@ Key findings:
 Scope: [1 paragraph from the worker ABSTRACT]
 
   ## Findings
-[Findings with in-text citations [1], [2, 3]]
+[Findings with cite-key markers [@pmid:...]; no bibliography - the ledger is
+the source of truth for citations]
 
   ## Tool / Query Log
 [tool + key arguments, e.g. article_search(query="...", dateRange="2021-01-01/", limit=15)]
 
   ## Evidence Gaps
 [queries that failed after retries, with reasons]
-
-  ## References
-[numbered bibliography]
 ```
 
 ## Citation placement rules
 
-- In-text: [1] single; [2, 3] list; [1-5] range - numbered by ORDER OF
-  APPEARANCE across the document.
+- Authored text uses semantic cite-key markers `[@pmid:...]`, groups
+  `[@a; @b]`; `render` (SKILL.md Step 5b) numbers them by ORDER OF
+  APPEARANCE across the document and range-compresses groups.
 - The Executive Summary cites only the most critical sources.
-- Every table row with a number has a Source column.
-- Bibliography is ordered by number, not alphabetized.
+- Every table row with a number has a Source column (cite-key markers).
+- The References section is generated by `render` from the merged ledger and
+  ordered by number, not alphabetized.
 
 ## Provenance standard
 
@@ -100,15 +101,16 @@ combination [4]."
 
 - [ ] All six sections present, in order
 - [ ] Every claim has provenance (citation / source / method)
-- [ ] All in-text [N] present in References; no orphan references
+- [ ] Draft authored with cite-key markers; `render` exited 0 (all keys
+      resolved, no [MISSING ...] entries)
+- [ ] `vet-references.py` structural audit PASS (contiguous [1]..[N], N ==
+      bibliography count, no placeholders)
 - [ ] Identifiers included in references (PMIDs, DOIs, NCT IDs, patent IDs, accessions)
 - [ ] Access dates for web/official-site sources
 - [ ] Limitations honest about gaps and auth-gated tools not used
-- [ ] Findings re-numbered into one bibliography in final_report.md
-- [ ] References vetted against NCBI via vet-references.py (volume, issue, pages backfilled)
-- [ ] References generated from evidence/sources.jsonl (ledger-first: every
-      entry copied from a ledger record - worker-protocol rule 8, Step 5a)
 - [ ] Conflicting findings surfaced, not silently dropped
+- [ ] Findings obey the plan's inclusion/exclusion boundaries and the
+      evidence-verification discipline (analysis-methods.md)
 
 ## Common mistakes
 

package/skills/bioresearcher-deep-research/references/tool-selection.md

@@ -68,6 +68,8 @@ QUESTION TYPE
 ├─ Orthologues / consequences / regions / structures
 │   → ensembl_lookup / ensembl_homology / ensembl_consequence / ensembl_region
 │   → pdb (query | pdb_id | pdb_id+download)
+│      - Cite structure: dataset [@pdb:XXXX]
+│      - Cite paper: chain summary.pmid -> article_get(pmid) -> article [@pmid:XXXX]
 │   → details: references/ensembl-pdb.md
 │
 ├─ Ambiguous / multi-entity free text ("BRAF V600E melanoma")

package/skills/bioresearcher-deep-research/references/worker-protocol.md

@@ -17,35 +17,46 @@ clarification and plan review are exclusively the orchestrator's domain (SKILL.m
 TOPIC: <TOPIC>
 YOUR RESEARCH FOCUS: <RESEARCH-ASPECT>
 DESCRIPTION: <ABSTRACT>
+SKILL_DIR: <absolute skill dir>   # Tier B only; resolve before dispatch
+EXECUTION RULE: Do NOT read or inspect evidence-ledger.py or other skill scripts; all schemas and commands are fully specified here.
 ```
 
-- ABSTRACT: <200 words describing the exact focus of the aspect and a list of
-  detailed research items to investigate.
+- ABSTRACT: <200 words describing the exact focus, a list of detailed
+  research items to investigate, and the aspect's inclusion definition +
+  binding exclusion criteria (negative examples welcome). Numeric caps
+  inside it (source limits, call budgets) are binding on the worker.
 - Tier B (generic subagent): the orchestrator should ALSO inline into the
   prompt the Worker Rules below, the per-domain tool cheatsheet from
-  `references/tool-selection.md`, and the citation format summary from
-  `references/citations.md` - generic subagents may not have access to this
-  skill's files.
+  `references/tool-selection.md`, the cite-key marker summary from
+  `references/citations.md`, and the evidence-verification discipline from
+  `references/analysis-methods.md` - generic subagents may not have access
+  to this skill's files. The template's `SKILL_DIR` line carries the
+  resolved absolute script path.
 - Tier A (dedicated `bioresearcher-dr-worker` plugin subagent): the worker
-  reads this file plus `references/tool-selection.md` and
-  `references/citations.md` itself at startup (via
-  `${CLAUDE_PLUGIN_ROOT}`); the orchestrator sends ONLY the filled-in
-  template below.
+  reads this file plus `references/tool-selection.md`,
+  `references/citations.md`, and `references/analysis-methods.md` itself at
+  startup (via `${CLAUDE_PLUGIN_ROOT}`); the orchestrator sends ONLY the
+  filled-in template below.
 
 ## File protocol
 
-- Output files (exactly TWO):
+- Output files (exactly TWO - together they are the self-contained
+  deliverable for the aspect):
   - `reports/<TOPIC>/<YOUR-FOCUS>.md` — the aspect report, where `<YOUR-FOCUS>`
     is the underscore-separated aspect name (e.g. `clinical_landscape.md`).
   - `reports/<TOPIC>/evidence/<YOUR-FOCUS>.jsonl` — the evidence ledger, one
-    JSON record per potentially-citable source (see Worker rule 8).
+    JSON record per potentially-citable source (see Worker rule 8). The
+    ledger supplies every bibliography entry later; the pair
+    (report + ledger) must be understandable without any other context.
 - The write tool auto-creates parent directories - never use bash mkdir.
-- The report file must be self-contained: a reader should understand the
-  findings, the tools/queries used, and the sources cited without any other
-  context.
 - Report file structure: title, one-paragraph scope summary, findings with
-  in-text citations, tool/query log (which biomcp tools + key argument
-  values), and a full bibliography.
+  cite-key markers, tool/query log (which biomcp tools + key argument
+  values), and explicit evidence gaps. No bibliography section - the
+  orchestrator's `render` step generates numbering and References from the
+  ledger.
+- The ABSTRACT the orchestrator sends you defines the aspect's inclusion
+  definition and binding exclusion criteria; apply them per
+  `references/analysis-methods.md` (criterion vs keyword).
 
 ## Worker rules
 
@@ -60,9 +71,11 @@ DESCRIPTION: <ABSTRACT>
    and GEO supplementary downloads, which are unthrottled - space those out.
 4. No internal knowledge: use only biomcp tool results or official sources.
    If evidence is missing after retries, say so explicitly in the report.
-5. Citations: every claim gets [N] references; keep a numbered bibliography in
-   `references/citations.md` format. Capture identifiers as you go: PMIDs,
-  PMCIDs, DOIs, NCT IDs, patent IDs, GEO/SRA accessions, database IDs.
+5. Citations: every claim gets a semantic cite-key marker - `[@pmid:21639808]`,
+   groups `[@pmid:a; @nct:NCT00000000]` - using the keys the ledger actually
+   derived (the `add` banner echoes them). Capture identifiers as you go:
+   PMIDs, PMCIDs, DOIs, NCT IDs, patent IDs, GEO/SRA accessions, database IDs.
+   Never hand-number citations and never write a bibliography.
 6. Retry logic: if a query fails, wait a few seconds, retry with a simpler
    query; at most 3 attempts per query before recording the gap and moving on.
 7. Writing: succinct, accurate, professional - academic standard.
@@ -89,9 +102,10 @@ DESCRIPTION: <ABSTRACT>
       {"schema":"bioresearcher-evidence/1","type":"gene","ids":{"ncbi_gene":"673","hgnc":"HGNC:1097"},"title":"B-Raf proto-oncogene, serine/threonine kinase","meta":{"symbol":"BRAF"},"url":"https://www.ncbi.nlm.nih.gov/gene/673","provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"variant","ids":{"clinvar":"13961","rs":"rs113488022"},"title":"NM_004333.6(BRAF):c.1799T>A","meta":{"gene":"BRAF","protein_change":"V600E","significance":"Pathogenic"},"provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"drug","ids":{"chembl":"CHEMBL1229517"},"title":"vemurafenib","meta":{"indication":"BRAF V600E-mutant melanoma","source_section":"FDA label (drug_get safety section)"},"provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"disease","ids":{"mondo":"MONDO:0002025"},"title":"Cutaneous melanoma","url":"https://monarchinitiative.org/MONDO:0002025","provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"geo":"GSE12345"},"title":"Series title","provenance":[...]}
-      {"schema":"bioresearcher-evidence/1","type":"web","ids":{"url":"https://..."},"title":"Page Title","meta":{"organization":"FDA","accessed":"2026-09-10"},"provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"disease","ids":{"mondo":"MONDO:0002025"},"title":"Cutaneous melanoma","url":"https://monarchinitiative.org/MONDO:0002025","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"geo":"GSE12345"},"title":"Series title","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"dataset","ids":{"pdb":"6N65"},"title":"KRAS G-quadruplex G16T mutant","meta":{"method":"X-RAY DIFFRACTION","resolution":"1.6 Å"},"url":"https://www.rcsb.org/structure/6N65","provenance":[...]}
+       {"schema":"bioresearcher-evidence/1","type":"web","ids":{"url":"https://..."},"title":"Page Title","meta":{"organization":"FDA","accessed":"2026-09-10"},"provenance":[...]}
       {"schema":"bioresearcher-evidence/1","type":"other","ids":{"url":"https://..."},"title":"Any other citable source (FDA page, guideline, ...)","provenance":[...]}
       ```
 
@@ -103,19 +117,89 @@ DESCRIPTION: <ABSTRACT>
       take the standard retry ladder (rule 6), then leave the record in the
       ledger with a gap note in the aspect file - the orchestrator's verify
       step backfills what it can.
-    - With Bash available: append with
-      `python3 <skill_dir>/scripts/evidence-ledger.py add <file> --stdin`,
-      passing a JSON ARRAY of the batch's records (a heredoc works well), or
-      equivalently `add <file> @<batch.json>` with an array file. Both
-      validate, normalize, and accept every record in one call. A single
-      inline `'<record JSON>'` argument remains fine for one-off records.
-      Do NOT issue one `add` per record and do NOT write per-record scratch
-      files first - every append is a tool call (an LLM turn), so batch per
-      search result. Without Bash: write raw JSONL lines with the Write
-      tool; the orchestrator's merge validates them.
-    - BEFORE writing the bibliography, RE-READ your ledger file; compose
-      every References entry by COPYING ledger fields. A bibliography entry
-      must not contain any field absent from the ledger.
+    - PDB dual-entity discipline: when querying `pdb`, distinguish between
+      citing the macromolecular structure and citing the associated publication:
+      - To cite the published paper: set `type: "article"` with `ids.pmid` (or
+        `ids.doi`). NEVER copy `summary.title` (structure title) or
+        `summary.authors` (deposition list) from the PDB result into the
+        article record. Enrich via `article_get(pmid)` for canonical article
+        metadata, or leave title/authors null for orchestrator verification.
+      - To cite the 3D structure itself: set `type: "dataset"` with `ids.pdb:
+        "<PDB_ID>"` and `title: summary.title`. Canonical key derived:
+        `pdb:<PDB_ID>`. Marker: `[@pdb:<PDB_ID>]`.
+    - With Bash available (the orchestrator provides `SKILL_DIR` in the
+      prompt): append with
+      `python3 <SKILL_DIR>/scripts/evidence-ledger.py add <file> --stdin`,
+      substituting the SKILL_DIR value from your prompt LITERALLY - it is a
+      path string, NOT an environment variable (`$SKILL_DIR` in a shell
+      resolves to nothing and breaks the call). Pass records via a shell heredoc
+      or with an array/JSONL file (`add <file> @<batch.json>`):
+      ```bash
+      python3 <SKILL_DIR>/scripts/evidence-ledger.py add reports/<TOPIC>/evidence/<YOUR-FOCUS>.jsonl --stdin << 'EOF'
+      [
+        {"schema":"bioresearcher-evidence/1","type":"article","ids":{"pmid":"..."},"title":"...","provenance":[{"aspect":"<YOUR-FOCUS>","tool":"article_search","args":{},"retrieved_at":"<ISO>"}]}
+      ]
+      EOF
+      ```
+      (A JSON array `[...]`, a single JSON object `{...}`, or newline-delimited JSONL lines are all accepted by `--stdin` or `@<file>`).
+      Both validate, normalize, and accept every record in one call, and the banner echoes
+      the derived canonical keys - cite those keys. Re-adding the same key
+      MERGES fill-only (never overwrites a non-null value): later adds for
+      the same source are safe and expected (e.g. enriching a record after a
+      `_get` call), and a key that lives only in another aspect's ledger is
+      remedied by re-adding the record to your OWN ledger. Do NOT issue one
+      `add` per record and do NOT write per-record scratch files first -
+      every append is a tool call (an LLM turn), so batch per search result.
+      `retrieved_at` carries the real UTC time of the call (e.g.
+      `date -u +%Y-%m-%dT%H:%M:%SZ`) - never a rounded or placeholder
+      timestamp. Fields the tool did not return stay null; values inferred
+      from your own query parameters (e.g. a phase filter) may enter `meta`
+      ONLY with the filter captured in `provenance.args` and the inference
+      disclosed in the report. When querying ClinicalTrials.gov
+      (`trial_search` / `biomcp_trial_search`), use exact uppercase underscore
+      enum values for `status`: `RECRUITING`, `ACTIVE_NOT_RECRUITING`,
+      `COMPLETED`, `TERMINATED` (commas or spaces in status trigger HTTP 400
+      Bad Request from ClinicalTrials.gov). Without Bash ONLY (e.g. the Claude
+      plugin worker): write raw JSONL lines with the Write tool and re-read the
+      ledger to match markers; the orchestrator validates via `check` upon return.
+    - BEFORE reporting completion, run
+      `python3 <SKILL_DIR>/scripts/evidence-ledger.py check <file> --markers <YOUR-FOCUS>.md` -
+      it must exit 0: no quarantined lines, and every `[@key]` marker in
+      your aspect file resolves to a ledger record (markers are ONLY for
+      resolvable cited sources - a mention-by-id in prose stays plain text,
+      e.g. "the pivotal trial, NCT02435849, was not found"). Without Bash,
+      re-read the ledger and match the markers manually.
+9. Evidence quality: apply the evidence-verification discipline
+   (`references/analysis-methods.md`) to every claim - direction of
+   causality, quantitative fidelity, criterion vs keyword, axis discipline,
+   primary vs downstream.
+
+## Restart / gap top-up (orchestrator-dispatched)
+
+Aspect-file ownership is SERIALIZED, never concurrent: a top-up worker
+adopts the original worker's contract only after that worker has terminated.
+The orchestrator dispatches it when `evidence-ledger.py check` fails or for evidence gaps:
+
+- Target scope: touch ONLY `reports/<TOPIC>/<ASPECT>.md` and
+  `reports/<TOPIC>/evidence/<ASPECT>.jsonl`. Never edit other aspects or the
+  synthesis draft.
+- For unresolved markers: fetch canonical metadata via biomcp (`article_get`,
+  `trial_get`) and append via `add`. If no valid source exists, remove or
+  qualify the claim in `<ASPECT>.md` and document the gap under `## Evidence Gaps`.
+  Never invent or guess cite-keys.
+- For quarantined lines: fix the JSON formatting in the ledger.
+- End with `check <file> --markers <aspect>.md` (exit 0) before reporting.
+
+### Remediation worker prompt template
+
+```md
+TOPIC: <TOPIC>
+YOUR RESEARCH FOCUS: <RESEARCH-ASPECT> (REMEDIATION)
+DIAGNOSTIC OUTPUT:
+<stdout and stderr from: evidence-ledger.py check reports/<TOPIC>/evidence/<ASPECT>.jsonl --markers reports/<TOPIC>/<ASPECT>.md>
+TASK: Resolve quarantined lines in reports/<TOPIC>/evidence/<ASPECT>.jsonl and fetch canonical metadata for unresolved markers via biomcp. Touch no other aspects or synthesis files. End with `evidence-ledger.py check` (must exit 0).
+SKILL_DIR: <absolute path to this skill's directory>
+```
 
 ## Retry ladder (per query)
 
@@ -135,8 +219,8 @@ attempt 3: alternate tool/source (see references/tool-selection.md routing)
   inlined cheatsheet (Tier B). Do not mix tiers within one topic.
 - Launch workers in parallel in batches of up to 5.
 - Track each aspect in the todo list; mark complete when its output file
-  exists, ends with a bibliography, AND its evidence ledger file exists with
-  at least one record per cited source.
+  exists with cite-key markers throughout AND its evidence ledger file
+  exists, passes `check --markers` (exit 0), and covers every cited key.
 - If a worker fails or stalls, restart it (same prompt), max 3 restarts.
 - Tell the user up front: "If subagents are stuck without progress for too
   long, interrupt and ask me to resume work."
@@ -147,8 +231,8 @@ If the harness has no subagent/Task tool, the SAME protocol runs inline in the
 main conversation, one aspect at a time:
 
 1. Announce the aspect being worked on.
-2. Apply Worker rules 2-8 exactly (same tool selection, retries, citation
-   discipline, evidence ledger, file protocol).
+2. Apply Worker rules 2-9 exactly (same tool selection, retries, citation
+   discipline, evidence ledger, evidence quality, file protocol).
 3. Write `reports/<TOPIC>/<ASPECT>.md` and
    `reports/<TOPIC>/evidence/<ASPECT>.jsonl` before moving to the next aspect.
 4. After the last aspect, proceed to synthesis (SKILL.md Step 5).
@@ -160,10 +244,14 @@ Sequential mode trades latency for context - keep per-aspect tool calls lean
 
 - [ ] Output file exists at `reports/<TOPIC>/<ASPECT>.md`
 - [ ] Evidence ledger exists at `reports/<TOPIC>/evidence/<ASPECT>.jsonl`
-      with at least one record per cited source (rule 8)
+      and passes `evidence-ledger.py check <file> --markers <ASPECT>.md`
+      with exit 0 (Tier A without Bash: re-read the ledger and match the
+      markers manually)
+- [ ] Every cite-key marker `[@...]` used in the aspect file resolves to a
+      ledger record (no invented keys)
 - [ ] Every claim has a citation, source note, or method note
-- [ ] Bibliography present, numbered by order of appearance, every entry
-      copied from ledger fields (no field absent from the ledger)
+- [ ] Findings obey the aspect's inclusion/exclusion boundaries and the
+      evidence-verification discipline
 - [ ] Identifiers included (PMIDs / DOIs / NCT IDs / patent IDs / accessions)
 - [ ] Tool/query log included
 - [ ] Evidence gaps (if any) explicitly listed