psyclaw 0.27.22 → 0.28.0

package/vendor/ars/academic-paper/references/plan_mode_protocol.md

@@ -0,0 +1,112 @@
+# Plan Mode: Chapter-by-Chapter Guided Planning
+
+Core principle: From the perspective of a senior doctoral advisor and disciplinary methodology expert, guide users to think through every part of their paper chapter by chapter. Instead of writing directly, use Socratic dialogue to help users clarify what they want to write.
+
+```
+User: "guide my paper" / "help me plan my paper"
+     |
+=== Step 0: RESEARCH READINESS CHECK ===
+     |
+     +-> [socratic_mentor_agent] -> Confirm what materials the user already has
+         - "What research materials do you currently have? (literature, data, analysis results)"
+         - "Is your research question finalized? Can you state it in one sentence?"
+         -> If research foundation is lacking, recommend running deep-research (socratic mode) first
+     |
+=== Step 1: THESIS CRYSTALLIZATION ===
+     |
+     +-> [socratic_mentor_agent] -> Probe the core thesis
+         - "What is your paper arguing?"
+         - "How would someone who disagrees with you respond?"
+         - "After reading your paper, what should the reader think differently about?"
+         Extract [INSIGHT: thesis_statement]
+     |
+=== Step 2: CHAPTER-BY-CHAPTER NEGOTIATION ===
+     |
+     For each chapter (Introduction -> Literature -> Method -> Results -> Discussion -> Conclusion):
+     |
+     +-> [socratic_mentor_agent] -> Probe the purpose and content of each chapter
+     |
+     |   Introduction:
+     |   - "What sense of urgency should the reader feel by the end of this chapter?"
+     |   - "After reading the Introduction, what should the reader expect to see next?"
+     |   - "What is your research gap? State it in one sentence."
+     |
+     |   Literature Review:
+     |   - "How many stories are you telling? What is the relationship between them?"
+     |   - "What conclusion should your literature review ultimately lead to?"
+     |   - "Is there an important work you disagree with? Why?"
+     |
+     |   Methodology:
+     |   - "If someone challenges your method, how would you respond?"
+     |   - "Is there a simpler method that could also answer your question? Why didn't you choose it?"
+     |   - "What is the biggest limitation of your method? How do you handle it?"
+     |
+     |   Results:
+     |   - "What is your most important finding? State it in one sentence."
+     |   - "Were there any unexpected results? How do you explain them?"
+     |   - "Is there any evidence in your data that does not support your hypothesis?"
+     |
+     |   Discussion:
+     |   - "How do your results dialogue with existing literature?"
+     |   - "What is the one thing you most want the reader to remember?"
+     |   - "What recommendations does your research have for practice/policy?"
+     |
+     |   Conclusion:
+     |   - "If you could only leave one paragraph, what would you say?"
+     |   - "What future research directions does your study open up?"
+     |
+     At least 2 rounds of dialogue per chapter
+     After each chapter concludes, [socratic_mentor_agent] extracts a Chapter Summary
+     |
+     +-> [structure_architect_agent] -> Produce complete outline based on all Chapter Summaries
+     |
+=== Step 2.5: CONTRIBUTION SHARPENING ===
+     |
+     +-> [socratic_mentor_agent] -> Ask the user to articulate the contribution their
+         Chapter Summaries claim; when probing, quote only user-written text
+         Questions: the Layer-5 later-stage anchored forms L5-W1 / L5-W2 / L5-W3
+         (single-sourced in deep-research/agents/socratic_mentor_agent.md Layer 5 —
+         NOT this skill's agents/socratic_mentor_agent.md, which has no Layer 5;
+         see Source & Boundary below), anchored to the user's own Chapter Summaries
+         At least 1 round of dialogue
+         If the user articulates a contribution -> extract [INSIGHT: contribution_claim]
+         in the user's words; otherwise record the open contribution question and
+         carry it into Step 3 — never fill it in
+         Questions only — never propose, substitute, rank, expand, or select a
+         contribution claim for the user.
+     |
+=== Step 3: ARGUMENT STRESS TEST ===
+     |
+     +-> [socratic_mentor_agent + argument_builder_agent]
+         -> Probe evidence and logic for each sub-argument
+         -> "Where is the weakest point in this argument?"
+         -> "If you reverse your argument, does it still hold?"
+         -> Final output: Chapter Plan (with core argument, supporting evidence, expected word count per chapter)
+     |
+Output: Chapter Plan + INSIGHT Collection
+-> User can then use full mode to produce the complete paper
+-> Or use academic-paper-reviewer to review the Chapter Plan
+```
+
+## Plan Mode Activation Rules
+
+Activate `plan` mode (Socratic chapter-by-chapter guidance) when the user's **intent** matches any of the following patterns, **regardless of language**. Detect meaning, not exact keywords.
+
+**Intent signals** (any one is sufficient):
+1. User wants to be guided or led through paper writing, not just given a finished paper
+2. User asks for step-by-step or chapter-by-chapter planning
+3. User expresses uncertainty about how to start or structure a paper
+4. User is a first-time paper writer or explicitly says they are a beginner
+5. User has research results but doesn't know how to turn them into a paper
+6. User wants to think through each section before writing
+
+**Default rule**: When intent is ambiguous between `plan` and `full`, **prefer `plan`** — it is safer to guide a user who needs help than to produce a paper they can't use. The user can always switch to `full` later.
+
+**Example triggers** (illustrative, not exhaustive):
+"guide my paper", "help me plan my paper", "I don't know how to start", 「引導我寫論文」「幫我規劃論文」, or equivalent in any language
+
+## Step 2.5 Contribution Sharpening — Source & Boundary (v3.12, #393)
+
+**Single source of the questions.** Step 2.5 asks the later-stage anchored forms **L5-W1 / L5-W2 / L5-W3** defined under Layer 5 (SIGNIFICANCE & CONTRIBUTION) in `deep-research/agents/socratic_mentor_agent.md` — read the question text there. This protocol carries only the IDs and the local anchor (the user's own Chapter Summaries); it holds no question text of its own, so a Layer-5 edit propagates by reference instead of forking.
+
+**Boundary (Kong L2 verb test — `docs/design/2026-06-08-kong-255-l2-advisory-not-generation.md`).** Surface + ask only: the mentor may quote what the user already wrote in the Chapter Summaries and ask about it. It must never propose, substitute, rank, expand, or select a contribution claim; no scoring, no generated answers, no proposed reframings. `[INSIGHT: contribution_claim]` records the user's own words — if the user cannot answer, the open question is itself recorded and carried into Step 3, not filled in by the mentor.

package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md

@@ -0,0 +1,200 @@
+# Policy-Anchor Disclosure Protocol
+
+**Status**: #108 implementation (parented to Decision Doc 20ed72d)
+**Parent skill**: `academic-paper`
+**Mode name**: `disclosure` with `--policy-anchor=<a>` selector (parallel track to `--venue=<v>` v3.2 path; see `disclosure_mode_protocol.md` for the dispatch).
+**Anchor inventory**: `prisma-trAIce, icmje, nature, ieee` (closed enum; expansion via §4.7 deferred per Decision Doc §4.2).
+**Data source**: `policy_anchor_table.md` (read at runtime; LLM looks up the row for `--policy-anchor=<a>` × field-N).
+
+This protocol document is the runtime instruction set the LLM follows when the user invokes `disclosure` mode with a policy-anchor selector. It encodes the 8 Decision Doc §4.3 frozen invariants, the §3 G10 7-row precedence table for whole-disclosure output decision, the 11 §4.4 open-concern resolutions (per implementation spec §3), the auto-promotion forbiddance, and the per-anchor render flows (PRISMA-trAIce / ICMJE / Nature / IEEE).
+
+---
+
+## 0. Why this protocol exists
+
+ARS's v3.2 `disclosure` mode renders a venue-targeted applicability/status bundle (`REQUIRED`, `ACTION_ONLY`, `NOT_REQUIRED`, or `UNKNOWN`, plus typed fail-closed halt status; 15 policy targets as of the v2 database: ICLR, NeurIPS, Nature, Science, ACL, EMNLP, plus the #596 medical-publishing set — see `venue_disclosure_policies.md`). The 4-anchor `--policy-anchor=<a>` track instead uses the anchor-specific output contract below when the author targets a **policy anchor** (PRISMA-trAIce, ICMJE, Nature Portfolio, IEEE) rather than a specific journal venue. The two tracks coexist; v3.2 venue path remains the default for journal submissions.
+
+---
+
+## 1. Inputs
+
+1. **Paper draft** (same as v3.2): manuscript text plus pipeline log if available.
+2. **Selector**: `--policy-anchor=<a>` where `a ∈ {prisma-trAIce, icmje, nature, ieee}`. **Selector-mutually-exclusive by default** — supplying both `--policy-anchor` and `--venue` triggers the §5 conflict-resolution flow, which permits exactly one consistent pair (any Nature Portfolio venue + `--policy-anchor=nature`, sharing the canonical `shared/policy_data/nature_policy.md` source) and rejects every other combination with explicit error. See §5 for the full enumeration.
+3. **Pipeline signal**: `slr_lineage=true|false` set by the upstream pipeline orchestrator when an SLR-mode stage appears in the run history. Drives the §4.3 G2 invariant track gate (concern #1 resolution: explicit `slr_lineage` input).
+4. **Cold-start fallback**: when the renderer runs outside a pipeline (no `slr_lineage` set), the author supplies `mode=<value>` explicitly. Silent fallback to general track on missing input is **forbidden** by §4.3 G2 invariant.
+5. **v3.2 Phase 2 AI usage categorization**: the same input shape v3.2 uses. Each AI usage category carries state ∈ `{USED, NOT USED, UNCERTAIN}`.
+6. **Optional `ai_used: true | false`**: explicit author-supplied flag layered on top of category state. Composes with category state per §2 G10 7-row precedence table below.
+7. **Tool identity per AI tool** (concern #2 resolution): auto-detected from session metadata (mirror v3.2 `disclosure_mode_protocol.md` Phase 4 detection); explicit fallback per tool when session metadata absent or non-Claude tools are involved.
+
+---
+
+## 2. Whole-disclosure decision — §3 G10 7-row precedence table
+
+Rows are evaluated in priority order from top to bottom; the renderer emits the output of the **first** row whose precondition matches. Subsequent rows do not fire. This table is the §4.3 **G3 / G10 invariant** in load-bearing form.
+
+Before evaluating this table, apply the shared Phase-2 intake-integrity gate in
+`disclosure_mode_protocol.md`: a `USED` `OTHER / UNCLASSIFIED` category halts
+until the author maps it to an executable category. Row 4 cannot render from an
+unclassified-use record; emit an honest "AI-disclosure intake incomplete —
+unclassified use requires author mapping" annotation instead. The same
+intake-pending annotation applies when the shared external-use inventory is not
+author-confirmed.
+
+| # | Precondition (first match wins) | Whole-disclosure output |
+|---|---|---|
+| 1 | `ai_used: false` supplied AND ≥1 v3.2 category is USED (contradiction) | Honest "AI-disclosure conflict — explicit no-AI input contradicts USED category" annotation; renderer prompts the user to reconcile before any anchor render emits. |
+| 2 | `ai_used: false` supplied AND no v3.2 category is USED AND no v3.2 category is UNCERTAIN | "No AI was used in preparing this paper" statement (G10 opt-in path). |
+| 3 | `ai_used: false` supplied AND ≥1 v3.2 category is UNCERTAIN AND no v3.2 category is USED | Honest "AI-disclosure tension — explicit no-AI input but categories still UNCERTAIN" annotation; renderer prompts the user to resolve UNCERTAIN before emitting the no-AI statement. |
+| 4 | `ai_used: true` supplied OR ≥1 v3.2 category is USED, AND row 1 did not match | Full anchor-specific disclosure render per §3 below, applying the **concern #6 resolution** (USED facets at full strength; per-facet "AI disclosure pending — category {X} not confirmed; resolve via v3.2 Phase 2" annotation immediately after each still-UNCERTAIN facet's render slot). |
+| 5 | ≥1 v3.2 category is UNCERTAIN AND no v3.2 category is USED AND no `ai_used` input | Honest "AI-disclosure status not supplied — categories pending confirmation" annotation; renderer prompts the user to run the v3.2 UNCERTAIN-confirmation flow before re-invoking. |
+| 6 | ≥1 v3.2 category supplied AND every supplied category is NOT USED AND no UNCERTAIN AND no `ai_used` input | Silence — emit no AI-disclosure statement at all (G10 "silence is default-OK"). |
+| 7 | None of rows 1–6 match (empty input across every dimension) | Honest "AI-disclosure status not supplied for this run" annotation (G3 D3 pure cold-start). |
+
+**Concern #10 resolution (`ai_used: true` substantive-content gate):** when `ai_used: true` is supplied **and no v3.2 category is marked USED** (regardless of whether Phase 2 has been performed — i.e., this gate fires for both "bare-flag input only, no categorization" **and** "Phase 2 done but every category came back NOT USED while `ai_used:true` is still set"), row 4 does not emit a complete render. Instead, the input is treated as a **prompt-trigger** that halts the current run and asks the user to reconcile: either supply a USED category, change `ai_used` to false, or run / re-run v3.2 Phase 2 categorization. Once a USED category is supplied (or `ai_used` flipped), re-evaluate against the §2 table from the top. This implements the concern #10 resolved path: "force v3.2 categorization flow", consistent with concern #6's honest-signal-preservation discipline. The forbiddance: emitting a full anchor disclosure with `ai_used:true` and zero USED facets.
+
+---
+
+## 3. Per-anchor render flows
+
+For each anchor, the renderer reads `policy_anchor_table.md` rows 1..16 and applies the field-level rules below. The 4 anchors share the row-4 dispatcher above; the per-anchor sections only describe **what to emit** after row 4 fires.
+
+### 3.1 `--policy-anchor=prisma-trAIce`
+
+**Track gate (G2 invariant):** this anchor is only valid when `slr_lineage=true` (pipeline signal) or `mode=systematic-review` (cold-start input). Selecting `--policy-anchor=prisma-trAIce` with `slr_lineage=false` is non-conformant — the renderer refuses with an explicit error citing the G2 invariant.
+
+**G5 invariant — three gates for M6 prompt disclosure:** PRISMA-trAIce M6 prompt disclosure fires only when **all three** hold:
+1. PRISMA-trAIce track selected (the gate above).
+2. `tool_type ∈ {LLM, GenAI}` (per PRISMA M6 "if any" predicate).
+3. AI use is methodological-in-SLR (search / screening / data extraction / Risk of Bias / synthesis / drafting per PRISMA M3.a), **not pure copyediting**.
+
+When gate 3 fails (SLR manuscript whose only LLM use is editorial), the renderer routes to the §3.5 copyediting-carve-out path instead. PRISMA-trAIce track does not own the copyediting case.
+
+**Render fields:**
+- Per `policy_anchor_table.md` row 1–3: emit one **tool identity tuple** per AI tool (concern #2 resolution; auto-detect from session, fallback explicit). Identity tuple = (tool name, version if applicable, developer/provider).
+- Row 4–5: emit one **(tool × task) record** per (tool, task) tuple across the M3.a 6-stage enum (concern #3 resolution). Missing tuples produce "not supplied" annotation per tuple. Per-task prompt disclosure follows M6.a granularity.
+- Row 8: emit prompt records per (tool × task) tuple per gate G5.
+- Row 9: emit human oversight description per M8 sub-items.
+- Rows 11–12: emit performance evaluation method + results per M9 + R2 when applicable.
+- Row 13: emit limitations narrative per D1.
+- Row 14: distribute disclosure fragments per Table 1 row groupings (Title / Abstract / Introduction / Methods / Results / Discussion). The renderer emits per-section fragments, not a single paragraph.
+
+### 3.2 `--policy-anchor=icmje`
+
+**Track gate:** no SLR lineage requirement. Available regardless of `slr_lineage` value.
+
+**Render fields:**
+- Row 10 (explicit-mandate): emit ICMJE human-responsibility statement using the verbatim "humans are responsible for any submitted material that included the use of AI-assisted technologies" language. This sentence appears in **every** ICMJE render where row 4 fires.
+- Row 14 (explicit-recommend): emit two channels — cover letter (verbatim ICMJE language) + manuscript "appropriate section" (per the venue's submission policy). The two channels carry different paragraphs, not a single duplicated paragraph.
+- Row 16 (explicit-mandate): emit the text-attribution clause: appropriate attribution and full citations for AI-quoted material + the prohibition against citing AI-generated material as primary source. Surface this paragraph even when no images are involved (rule covers text-attribution).
+- Rows with `not-addressed` strength (9/16 cells): the renderer skips these by default; if v3.2 Phase 2 provides a category USED that would be served by such a field, surface a "ICMJE delegates this detail to journal-level policy; consider the v3.2 venue track for journal-specific phrasing" annotation.
+
+### 3.3 `--policy-anchor=nature`
+
+**Track gate:** no SLR lineage requirement.
+
+**Dedup with v3.2 Nature venue path:** the Nature substantive policy text is co-cited from `shared/policy_data/nature_policy.md` (canonical source pointer). Both consumers — the v3.2 Nature venue renderer in `venue_disclosure_policies.md` and this Nature anchor renderer — derive their substantive content from that shared source. **G4 invariant**: edits to Nature-specific policy quotes must go through the shared source first, never directly into either consumer.
+
+**Render fields:**
+- Rows 9–10 (both explicit-mandate): emit the human-accountability statement using Nature's "In all cases, there must be human accountability for the final version of the text" verbatim language. Combine with the authorship-rejection clause from row 10's second quote when the manuscript proposes any AI co-authorship.
+- Row 14 (explicit-recommend): emit Methods-section placement instruction citing the verbatim "Methods section (and if a Methods section is not available, in a suitable alternative part)" language.
+- Row 15 (explicit-recommend) carve-out semantics: **eliminate** strength. Copyediting-only use produces **no disclosure paragraph**, only an internal renderer log entry. The §4.3 G7 invariant forbids collapsing this into a boolean shared with IEEE's downgrade semantics.
+- Row 16 (explicit-mandate) image-rights handling: concern #5 resolution = **hybrid (annotation block + suggested inline patches)**. The renderer emits two outputs:
+  1. A standalone `image_disclosure_instructions.md` block describing, per image, which Nature carve-out applies (or default-deny) and what Nature label text appears in the image field.
+  2. A suggested patch diff against manuscript source figure metadata (caption, alt-text, image-field caption) for the author to optionally apply. **ARS does not modify manuscript source autonomously**; the patch is suggested-only.
+
+### 3.4 `--policy-anchor=ieee`
+
+**Track gate:** no SLR lineage requirement.
+
+**G8 invariant — paired mandate:** IEEE row 5 (`Specific task within stage`, explicit-mandate) and row 6 (`Affected manuscript sections / content locator`, explicit-mandate) are a paired mandate. The renderer emits **both** inputs together. Emitting `level_of_involvement` (row 5 narrative annotation) without an `affected_sections` locator (row 6) — or vice versa — is **non-conformant**.
+
+**Concern #4 resolution (IEEE section locator shape):** free-form list with recommended IMRaD exemplars. Accepted values: `"Introduction" | "Methods" | "Results" | "Discussion" | "Abstract" | "Title" | free-form-other`. Closed-enum would over-constrain IEEE's "brief explanation" language; free-form preserves the policy's narrative invitation. Test fixture covers both exemplar-match and free-form-other inputs.
+
+**Render fields:**
+- Row 1 (explicit-mandate): emit "The AI system used shall be identified" formulation — name + identifier per AI tool.
+- Rows 5–6 (paired explicit-mandate per G8): emit `affected_sections` list + `level_of_involvement` narrative annotation **together**.
+- Row 14 (explicit-mandate): emit placement instruction citing "acknowledgments section of any article submitted to an IEEE publication" verbatim. **No Methods placement, no cover-letter channel** — the tightest closed enum across all four anchors.
+- Row 15 (explicit-recommend) carve-out semantics: **downgrade-not-eliminate** strength. Copyediting-only use still produces a disclosure paragraph at the same acknowledgments location, but with recommend-strength rather than mandate language. The §4.3 G7 invariant forbids collapsing this into a boolean shared with Nature's eliminate semantics.
+- Row 16 (implicit): images/figures/code fold into the same acknowledgments-disclosure mandate as text. **No separate image-rights regime, no default-prohibition** (contrasts with Nature). The renderer emits a single acknowledgments paragraph covering all content types per IEEE policy. The §4.3 G9 invariant: each anchor's image-rights regime stays distinct; IEEE's fold-into-acknowledgments path does not merge with Nature's default-deny regime.
+
+### 3.5 Copyediting carve-out cross-anchor handling
+
+Per §4.3 G7 invariant + §4.5 / §4.6 cell #15, the copyediting carve-out semantics are anchor-specific:
+
+- **Nature anchor**: eliminate strength — no disclosure paragraph for copyediting-only use.
+- **IEEE anchor**: downgrade-not-eliminate — disclosure still emitted at acknowledgments, with recommend-strength language ("is recommended" rather than "shall be disclosed").
+- **PRISMA-trAIce anchor**: not in scope (M6 G5 gate 3 routes copyediting cases away from PRISMA-trAIce track entirely; see §3.1).
+- **ICMJE anchor**: not-addressed in the policy text; the renderer treats copyediting cases per the same path as substantive AI use (no carve-out, full ICMJE render).
+
+The renderer MUST NOT collapse these four behaviors into a single boolean `exempted_uses: [copyediting]` field — doing so would silently lose the eliminate-vs-downgrade-vs-not-in-scope distinctions.
+
+---
+
+## 4. Auto-promotion forbiddance (§4.3 G3 / G10 invariant)
+
+A still-UNCERTAIN category MUST NOT be rendered as though USED in any of the four anchor outputs. This is the load-bearing constraint behind concern #6's resolution: USED facets render at full strength; UNCERTAIN facets surface the per-facet annotation, never the full-strength render. The renderer MUST surface UNCERTAIN as UNCERTAIN throughout the disclosure text; silent promotion of any UNCERTAIN category to USED is **forbidden**.
+
+The test suite covers this forbiddance with negative fixtures asserting that an input with `ai_used:true` + 1 UNCERTAIN category + 0 USED categories does NOT emit a full-strength render of the UNCERTAIN category.
+
+---
+
+## 5. Venue + anchor conflict resolution (concern #7)
+
+When the user passes both `--venue=<v>` and `--policy-anchor=<a>`, the renderer evaluates whether the two map to compatible policies. The consistent-pair recognition for the Nature track covers the full Nature Portfolio venue family:
+
+- **Consistent — Nature Portfolio venue + `--policy-anchor=nature`**: includes canonical labels `{"Nature", "Nature Portfolio", "Nature (Nature Publishing Group)", "Nature Publishing Group"}` **and** any venue whose name starts with the prefix `"Nature "` (e.g., `Nature Medicine`, `Nature Communications`, `Nature Climate Change`, `Nature Energy`, `Nature Methods`, ...). All Nature Portfolio journals inherit the same parent AI policy, so each of these venue strings + `--policy-anchor=nature` proceeds via the shared source pointer.
+- **Conflicting — any other (venue, anchor) pair**: e.g., `--venue=Nature` + `--policy-anchor=IEEE`, `--venue=ICLR` + `--policy-anchor=icmje`, or a Nature Portfolio venue with a non-nature anchor → **reject with explicit error** listing the policy conflict and the canonical Nature consistent-pair definition above.
+
+Silent precedence is **forbidden** (Decision Doc §4.4 #7 + concern #7 resolution). The renderer must surface the conflict to the user and require an explicit selector choice. The recognition logic above is mirrored by the conformance referee's `is_nature_portfolio_venue()` helper in `scripts/policy_anchor_disclosure_referee.py` — when this protocol text drifts from that helper, the alignment is a non-conformance.
+
+---
+
+## 6. Three-state input completeness flag (concern #8)
+
+The §2 G10 7-row table evaluates first-match across (`ai_used` × per-category-state). Field-level computation:
+
+- `ai_used` ∈ `{true, false, unset}`.
+- Each v3.2 category ∈ `{USED, NOT USED, UNCERTAIN, not-supplied}`.
+- First-match-wins evaluation across §2's 7 rows.
+- Row-4 partial-state composition per concern #6 resolution: USED at full strength; per-facet annotation for each still-UNCERTAIN; auto-promotion forbidden.
+
+The §4.3 invariants constrain the evaluation:
+- **G1 invariant** — no `ai_disclosure` field is read from / written to the corpus entry schema; all input flows through the renderer's runtime input contract.
+- **G2 invariant** — track selection reads `slr_lineage` first, never derives SLR-status from `origin_mode` alone.
+- **G3 / G10 invariant** — the 7-row table holds; auto-promotion forbidden.
+- **G4 invariant** — 4 anchors, Nature dedup via shared source.
+- **G5 invariant** — three gates for M6 prompts.
+- **G7 invariant** — anchor-specific carve-out semantics.
+- **G8 invariant** — IEEE paired-mandate (row 5 + row 6).
+- **G9 invariant** — anchor-specific image-rights regimes.
+
+---
+
+## 7. §4.4 concern resolutions reference
+
+For audit traceability, this protocol implements each Decision Doc §4.4 open concern as follows. See implementation spec §3 for full rationale.
+
+- **concern #1** — Track-selection lookup mechanism resolved as: explicit `slr_lineage` input from pipeline orchestrator; cold-start `mode=` parameter.
+- **concern #2** — Tool identity collection: auto-detect from session metadata (v3.2 Phase 4 pattern); explicit fallback per tool for cold-start or non-Claude pipelines.
+- **concern #3** — Prompt scope: per-(tool × task) tuple across M3.a 6-stage enum; missing tuples emit "not supplied" annotation per tuple.
+- **concern #4** — IEEE section locator: free-form list with recommended IMRaD exemplars; parallel to G8 `level_of_involvement` design.
+- **concern #5** — Nature image metadata + labelling: hybrid output channel — standalone annotation block + suggested inline manuscript patches; ARS does not modify manuscript source autonomously.
+- **concern #6** — UNCERTAIN per-facet finalization: USED facets render at full strength; UNCERTAIN facets surface per-facet annotation immediately after each render slot.
+- **concern #7** — Venue + anchor conflict: reject with explicit error citing the policy conflict; silent precedence forbidden.
+- **concern #8** — Three-state completeness flag: full spec encoded in §6 above.
+- **concern #9** — Test set scope: covers §4.3 8 invariants + §4.4 #1–#8 + #10 + #11; positive + negative fixture per resolved path / forbidden path.
+- **concern #10** — `ai_used: true` substantive-content gate: bare-flag input treated as prompt-trigger forcing v3.2 categorization flow before any anchor render.
+- **concern #11** — G1 invariant scope: §2.1 G1 Decision authoritative (no `ai_disclosure` field added to corpus entry schema); non-renderer code changes for §4.4 #1 pipeline-plumbing **permitted** (pipeline orchestrator setting `slr_lineage` is not corpus-schema mutation).
+
+---
+
+## 8. Related
+
+- Decision Doc: `../docs/design/2026-05-14-ai-disclosure-schema-decision.md`
+- Implementation spec: `../docs/design/2026-05-14-ai-disclosure-impl-spec.md`
+- Anchor data table (consumer of this protocol): `policy_anchor_table.md`
+- v3.2 disclosure mode protocol (parallel track): `disclosure_mode_protocol.md`
+- v3.2 venue disclosure policies (Nature dedup peer): `venue_disclosure_policies.md`
+- Shared Nature policy source (canonical pointer, forthcoming): `shared/policy_data/nature_policy.md`
+- Lint contract: `../../scripts/check_policy_anchor_protocol.py`
+- Conformance test suite: `../../scripts/test_policy_anchor_disclosure.py` (Task #7)

package/vendor/ars/academic-paper/references/policy_anchor_table.md

@@ -0,0 +1,157 @@
+# Policy Anchor Table
+
+**Status**: #108 implementation (parented to Decision Doc 20ed72d)
+**Parent skill**: `academic-paper`
+**Consumer**: `policy_anchor_disclosure_protocol.md` (the LLM-prose renderer reads this table at runtime when in `disclosure` mode with `--policy-anchor=<a>` selector).
+**Provenance**: cells below carry verbatim policy quotes lifted from the discovery doc §4.3-4.6 source-of-truth (`docs/design/2026-05-13-ai-disclosure-schema-discovery.md`). Each anchor section records its snapshot id + truncated sha256 so the lint validator can confirm provenance integrity. Live URLs may drift after capture; the wayback snapshot is canonical.
+
+**Lint contract**: `scripts/check_policy_anchor_table.py` enforces 4-anchor coverage, 16-field-per-anchor canonical order, source_strength enum membership, and verbatim-quote presence for mandate/recommend/conditional cells. Mutation tests live at `scripts/test_check_policy_anchor_table.py`.
+
+**Nature ↔ v3.2 venue de-dup**: the Nature anchor below shares its substantive policy content with the v3.2 Nature venue renderer in `venue_disclosure_policies.md`. Both files cross-reference the canonical source pointer `shared/policy_data/nature_policy.md` so a future single-source-of-truth refactor can byte-compare imported substrings without breaking either consumer. The dedup pointer presence is lint-enforced via `verify_nature_dedup_with_venue` in `check_policy_anchor_table.py`.
+
+**Forbidden by Decision Doc §4.3 (renderer must honour these):**
+- G1 — no `ai_disclosure` field is added to the corpus entry schema; the renderer reads this table at runtime, no schema change.
+- G9 — image-rights regimes stay anchor-specific; the renderer MUST NOT unify field #16 into a single boolean across the four tables.
+- The shared `shared/policy_data/nature_policy.md` source MUST live outside any anchor-specific or venue-specific file so neither consumer can drift unilaterally.
+
+---
+
+## Anchor: prisma-trAIce
+
+**Snapshot:** `prisma-trAIce:wayback=20260513075443` (sha256: f95fc59f…)
+**Anchor caveat:** PRISMA-trAIce is a **pre-Delphi proposal** (Holst et al. 2025). It has not undergone formal consensus; no item carries `explicit-mandate` strength. Item-level directives use reporting-guideline verbs ("describe", "report", "include") classified here as `explicit-recommend` within the proposed framework. The framework itself is `conditional-mandate` on "AI tool used as methodological tool in an SLR" — outside that condition the framework does not apply.
+**Track gate:** the renderer routes to this anchor only when the upstream pipeline (or cold-start `mode=` input) sets `slr_lineage=true`. See `policy_anchor_disclosure_protocol.md` §4.4 #1 resolution.
+
+| # | Field | Source strength | Verbatim quote | Locator | Value type |
+|---|---|---|---|---|---|
+| 1 | AI tool name | explicit-recommend | "For each AI tool or system used: a. Specify the name, version number (if applicable), and developer/provider." | Table 1, M2.a | narrative |
+| 2 | AI tool version | explicit-recommend | "Specify the name, version number (if applicable), and developer/provider." | Table 1, M2.a | narrative |
+| 3 | AI tool developer / manufacturer | explicit-recommend | "Specify the name, version number (if applicable), and developer/provider." | Table 1, M2.a | narrative |
+| 4 | Stage / phase of use | explicit-recommend | "For each AI tool, clearly describe: a. The specific SLR stage(s) where it was applied (e.g., search, screening, data extraction, Risk of Bias assessment, synthesis, drafting)." | Table 1, M3.a | narrative |
+| 5 | Specific task within stage | explicit-recommend | "b. The precise task(s) the AI was intended to perform at each stage." | Table 1, M3.b | narrative |
+| 6 | Affected manuscript sections / content locator | implicit | (inference passage) Items T1, A1, I1, R1, D1, D2 each prescribe a *manuscript section* for disclosure but the framework does not require an explicit per-task content-locator field. | Table 1 row headings | narrative |
+| 7 | Date(s) of use | not-addressed | — | — | — |
+| 8 | Prompts | explicit-recommend | "For each LLM/GenAI tool used, report: a. The full prompt(s) employed for each specific task. If prompts are extensive, provide a detailed description of their structure, key instructions, context provided..." | Table 1, M6.a | narrative |
+| 9 | Human oversight method | explicit-recommend | "Describe the process of human interaction with and oversight of the AI tool(s) at each stage: a. How many reviewers interacted with/validated the AI outputs for each task? b. Did reviewers work independently when validating AI outputs?" | Table 1, M8.a–g | narrative |
+| 10 | Human responsibility statement | not-addressed | — | — | — |
+| 11 | Performance evaluation method | explicit-recommend | "Describe methods used to evaluate the AI tool(s) performance for the specific tasks within the review (if applicable and feasible). This may include: a. The reference standard used for evaluation... b. The metrics used..." | Table 1, M9 | narrative |
+| 12 | Performance evaluation results | explicit-recommend | "Report the results of any performance evaluations of the AI tool(s) for the specific tasks within the review (as described in P-trAIce M9). Include quantitative results (see M9) and measures of agreement between AI and human reviewers if assessed." | Table 1, R2 | narrative |
+| 13 | Limitations / known failure modes | explicit-recommend | "Discuss any limitations encountered in using the AI tool(s) (eg, technical issues, biases identified, challenges in prompt engineering, unexpected outputs, limitations in AI performance for specific sub-tasks)." | Table 1, D1 | narrative |
+| 14 | Disclosure location | implicit | (inference passage) Each Table 1 item is row-categorized by manuscript section (Title / Abstract / Introduction / Methods / Results / Discussion), implying section-of-record per item. | Table 1 row groupings | narrative |
+| 15 | Copyediting exemption predicate | not-addressed | — | — | — |
+| 16 | AI-generated image / figure / content rights | implicit | (inference passage) "Describe how data handled by AI tools (input, output, intermediate data) was managed and stored, and any measures taken to ensure data privacy, security, and compliance with copyright or terms of service, especially when using third-party cloud-based AI tools." M10 covers copyright/terms-of-service compliance for *data handled by AI tools* without dedicated AI-generated content rights field. | Table 1, M10 | narrative |
+
+**Distribution:** 0 explicit-mandate / 10 explicit-recommend / 0 conditional-mandate / 3 implicit / 3 not-addressed / 0 unknown.
+**Renderer rules (PRISMA-trAIce track):**
+- Disclosure location: each Table 1 row's manuscript-section row label drives placement (Title / Abstract / Introduction / Methods / Results / Discussion). The renderer emits per-section disclosure fragments, not a single paragraph.
+- Per-(tool × task) prompt scope: M6.a says verbatim "for each specific task" — the renderer produces one prompt record per (tool, task) tuple across M3.a's six SLR stages (search / screening / data extraction / Risk of Bias / synthesis / drafting). Missing tuples emit "not supplied" annotation per tuple, not per tool.
+- PRISMA M6 prompt disclosure fires only when **all three** G5 gates hold: (i) PRISMA-trAIce track selected, (ii) `tool_type ∈ {LLM, GenAI}`, (iii) AI use is methodological-in-SLR (not pure copyediting). Gate (iii) fail routes to the G7 copyediting carve-out path.
+
+---
+
+## Anchor: icmje
+
+**Snapshot:** `icmje:wayback=20260513075516` (sha256: 52f9e6bc…)
+**Anchor caveat:** ICMJE Recommendations are **adopted** and used by 1000+ journals as baseline. Strength language is consistent ("should require" / "should describe" / "must ensure" / "is not acceptable"). The page on AI Use by Authors (§V.A) is two short paragraphs, deliberately framework-level. Many fields are `not-addressed` because ICMJE delegates section-level detail to individual journals.
+
+| # | Field | Source strength | Verbatim quote | Locator | Value type |
+|---|---|---|---|---|---|
+| 1 | AI tool name | implicit | (inference passage) "the journal should require authors to disclose at submission whether they used AI-assisted technologies (such as LLMs, chatbots, or image creators)". Tool identity implied by "such technology... how they used it" but no field-level naming requirement. | §V.A, paragraph 1 | narrative |
+| 2 | AI tool version | not-addressed | — | — | — |
+| 3 | AI tool developer / manufacturer | not-addressed | — | — | — |
+| 4 | Stage / phase of use | implicit | (inference passage) "Authors who use such technology should describe... how they used it". "How they used it" implies stage. | §V.A, paragraph 1 | narrative |
+| 5 | Specific task within stage | implicit | (inference passage — same source as #4) "how they used it" implies task-level description without explicit field. | §V.A, paragraph 1 | narrative |
+| 6 | Affected manuscript sections / content locator | not-addressed | — | — | — |
+| 7 | Date(s) of use | not-addressed | — | — | — |
+| 8 | Prompts | not-addressed | — | — | — |
+| 9 | Human oversight method | explicit-recommend | "Authors should carefully review and edit the AI-generated content as the output can be incorrect, incomplete, or biased." | §V.A, paragraph 1 | narrative |
+| 10 | Human responsibility statement | explicit-mandate | "Therefore, humans are responsible for any submitted material that included the use of AI-assisted technologies." | §V.A, paragraph 1 | narrative |
+| 11 | Performance evaluation method | not-addressed | — | — | — |
+| 12 | Performance evaluation results | not-addressed | — | — | — |
+| 13 | Limitations / known failure modes | not-addressed | — | — | — |
+| 14 | Disclosure location | explicit-recommend | "Authors who use such technology should describe, in both the cover letter and the submitted work in the appropriate section if applicable, how they used it" | §V.A, paragraph 1 | narrative |
+| 15 | Copyediting exemption predicate | not-addressed | — | — | — |
+| 16 | AI-generated image / figure / content rights | explicit-mandate | "Humans must ensure there is appropriate attribution of all quoted material, including full citations." + "Referencing AI-generated material as the primary source is not acceptable." | §V.A, paragraph 1 | narrative |
+
+**Distribution:** 2 explicit-mandate / 2 explicit-recommend / 3 implicit / 9 not-addressed / 0 unknown.
+**Renderer rules (ICMJE track):**
+- Disclosure location: two-channel — cover letter (cite ICMJE language verbatim) + manuscript "appropriate section". Renderer emits separate paragraphs per channel, not a single duplicated paragraph.
+- Field #10 mandate triggers a human-responsibility sentence using ICMJE's verbatim language. This sentence appears regardless of which other facets are USED, as long as at least one AI category is USED in the run.
+- Field #16 mandate produces a paragraph noting (a) appropriate attribution + full citations for AI-quoted material, (b) AI-generated material may not be cited as primary source. The renderer surfaces this paragraph even when no images are involved (the rule covers text-attribution).
+
+---
+
+## Anchor: nature
+
+**Snapshot:** `nature:wayback=20260513075542` (sha256: cf691cba…)
+**Source-of-truth pointer:** see `shared/policy_data/nature_policy.md` for the canonical substantive policy text; the v3.2 venue renderer (`venue_disclosure_policies.md` Nature entry) shares this source. **De-dup invariant:** edits to Nature-specific policy quotes must go through `shared/policy_data/nature_policy.md` first; both consumers re-cite from there. Lint contract enforced by `verify_nature_dedup_with_venue` in `check_policy_anchor_table.py`.
+**Anchor caveat:** Nature Portfolio AI editorial policy is **adopted** and applies across all Nature Portfolio journals. Author-facing surface covers four sections (AI authorship / Generative AI images / AI use by peer reviewers / Editorial use). ARS matrix covers author-side obligations only (AI authorship + Generative AI images). The policy is framework-level for text and prohibition-level for images (generative AI images banned by default with three carve-outs).
+
+| # | Field | Source strength | Verbatim quote | Locator | Value type |
+|---|---|---|---|---|---|
+| 1 | AI tool name | implicit | (inference passage) "Use of an LLM should be properly documented in the Methods section (and if a Methods section is not available, in a suitable alternative part) of the manuscript." Documentation requirement implies tool identity disclosure. | §AI authorship | narrative |
+| 2 | AI tool version | not-addressed | — | — | — |
+| 3 | AI tool developer / manufacturer | not-addressed | — | — | — |
+| 4 | Stage / phase of use | implicit | (inference passage) "Use of an LLM should be properly documented in the Methods section". "Use" implies stage/task description in Methods. | §AI authorship | narrative |
+| 5 | Specific task within stage | implicit | (inference passage — same source as #4) "properly documented in the Methods section" implies task-level description without dedicated field. | §AI authorship | narrative |
+| 6 | Affected manuscript sections / content locator | implicit | (inference passage) "in the relevant caption upon submission" for non-generative ML image tools; LLM text use implies Methods-section documentation. | §Generative AI images (caption rule); §AI authorship (Methods rule) | narrative |
+| 7 | Date(s) of use | not-addressed | — | — | — |
+| 8 | Prompts | not-addressed | — | — | — |
+| 9 | Human oversight method | explicit-mandate | "In all cases, there must be human accountability for the final version of the text and agreement from the authors that the edits reflect their original work." | §AI authorship | narrative |
+| 10 | Human responsibility statement | explicit-mandate | "an attribution of authorship carries with it accountability for the work, which cannot be effectively applied to LLMs" + "there must be human accountability for the final version of the text" | §AI authorship | narrative |
+| 11 | Performance evaluation method | not-addressed | — | — | — |
+| 12 | Performance evaluation results | not-addressed | — | — | — |
+| 13 | Limitations / known failure modes | not-addressed | — | — | — |
+| 14 | Disclosure location | explicit-recommend | "Use of an LLM should be properly documented in the Methods section (and if a Methods section is not available, in a suitable alternative part) of the manuscript." + (for non-generative ML on images) "should be disclosed in the relevant caption upon submission" | §AI authorship + §Generative AI images | narrative |
+| 15 | Copyediting exemption predicate | explicit-recommend | "The use of an LLM (or other AI-tool) for \"AI assisted copy editing\" purposes does not need to be declared." (partial-verbatim predicate) "AI-assisted improvements to human-generated texts for readability and style... [but] do not include generative editorial work and autonomous content creation." | §AI authorship | narrative |
+| 16 | AI-generated image / figure / content rights | explicit-mandate | "Springer Nature journals are unable to permit its use for publication." + "All exceptions must be labelled clearly as generated by AI within the image field." | §Generative AI images | narrative |
+
+**Distribution:** 3 explicit-mandate / 2 explicit-recommend / 0 conditional-mandate / 4 implicit / 7 not-addressed / 0 unknown.
+**Renderer rules (Nature track):**
+- Disclosure location: Methods section by default (or "suitable alternative" if Methods is not present in the manuscript type). Renderer emits placement instruction citing the verbatim "Methods section (and if a Methods section is not available, in a suitable alternative part)" language.
+- Field #15 carve-out semantics: **eliminate** strength — copyediting-only use produces **no disclosure paragraph**, only an internal log entry. Renderer MUST NOT collapse this into a boolean shared with IEEE's downgrade semantics (Decision Doc §4.3 G7 invariant).
+- Field #16 mandate: image-rights handled via the §4.4 #5 hybrid output channel. Renderer emits (a) standalone `image_disclosure_instructions.md` block describing per-image carve-out classification and Nature label text; (b) a suggested patch diff against manuscript source figure metadata (caption / alt-text / image-field caption) for the author to optionally apply. ARS does not modify manuscript source autonomously.
+
+---
+
+## Anchor: ieee
+
+**Snapshot:** `ieee:wayback=20260513075605` (sha256: 3ab8db50…)
+**Anchor caveat:** IEEE's guideline page (April 16, 2024) is **adopted** and applies across IEEE publications. Substantive policy is **two short paragraphs** (~150 words combined). 3 stacked mandates within paragraph 1; 1 recommend (copyediting carve-out) within paragraph 2. Notable absences vs other anchors: **no explicit human-responsibility statement** (contrasts with ICMJE/Nature), **no human-oversight requirement** (contrasts with Nature), **no image-rights regime distinct from text** (images/figures/code fold into general acknowledgments-disclosure rule).
+
+| # | Field | Source strength | Verbatim quote | Locator | Value type |
+|---|---|---|---|---|---|
+| 1 | AI tool name | explicit-mandate | "The AI system used shall be identified" | Paragraph 1, sentence 2 | narrative |
+| 2 | AI tool version | not-addressed | — | — | — |
+| 3 | AI tool developer / manufacturer | not-addressed | — | — | — |
+| 4 | Stage / phase of use | implicit | (inference passage) "accompanied by a brief explanation regarding the level at which the AI system was used to generate the content". "Level" reads as degree-of-involvement rather than SLR-style stage enum. | Paragraph 1, sentence 2 | narrative |
+| 5 | Specific task within stage | explicit-mandate | "specific sections of the article that use AI-generated content shall be identified and accompanied by a brief explanation regarding the level at which the AI system was used to generate the content" | Paragraph 1, sentence 2 | narrative |
+| 6 | Affected manuscript sections / content locator | explicit-mandate | "specific sections of the article that use AI-generated content shall be identified" | Paragraph 1, sentence 2 | narrative |
+| 7 | Date(s) of use | not-addressed | — | — | — |
+| 8 | Prompts | not-addressed | — | — | — |
+| 9 | Human oversight method | not-addressed | — | — | — |
+| 10 | Human responsibility statement | not-addressed | — | — | — |
+| 11 | Performance evaluation method | not-addressed | — | — | — |
+| 12 | Performance evaluation results | not-addressed | — | — | — |
+| 13 | Limitations / known failure modes | not-addressed | — | — | — |
+| 14 | Disclosure location | explicit-mandate | "shall be disclosed in the acknowledgments section of any article submitted to an IEEE publication" | Paragraph 1, sentence 1 | narrative |
+| 15 | Copyediting exemption predicate | explicit-recommend | "The use of AI systems for editing and grammar enhancement is common practice and, as such, is generally outside the intent of the above policy. In this case, disclosure as noted above is recommended." | Paragraph 2 | narrative |
+| 16 | AI-generated image / figure / content rights | implicit | (inference passage) "The use of content generated by artificial intelligence (AI) in an article (including but not limited to text, figures, images, and code) shall be disclosed in the acknowledgments section" — images/figures/code fold into the same acknowledgments-disclosure mandate as text; no separate image-rights regime. | Paragraph 1, sentence 1 | narrative |
+
+**Distribution:** 4 explicit-mandate / 1 explicit-recommend / 0 conditional-mandate / 2 implicit / 9 not-addressed / 0 unknown.
+**Renderer rules (IEEE track):**
+- Disclosure location: acknowledgments section only — the tightest closed enum across all four anchors. Renderer emits placement instruction citing the verbatim "acknowledgments section of any article submitted to an IEEE publication" language. **No Methods placement**, no cover-letter channel.
+- Field #5 + field #6 are a paired mandate (Decision Doc §4.3 G8 invariant). The renderer emits **both** a per-section locator input (free-form list with recommended IMRaD exemplars `"Introduction" | "Methods" | "Results" | "Discussion" | "Abstract" | "Title" | free-form-other`) **and** a `level_of_involvement` narrative annotation (G8 design). Emitting one without the other is non-conformant.
+- Field #15 carve-out semantics: **downgrade-not-eliminate** strength — copyediting-only use still produces a disclosure paragraph at the same acknowledgments location, but with recommend-strength rather than mandate language. Renderer MUST NOT collapse this into a boolean shared with Nature's eliminate semantics (Decision Doc §4.3 G7 invariant).
+
+---
+
+## Related
+
+- Decision Doc (parent): `docs/design/2026-05-14-ai-disclosure-schema-decision.md`
+- Implementation spec (parent): `docs/design/2026-05-14-ai-disclosure-impl-spec.md`
+- Discovery doc (verbatim quote source-of-truth): `docs/design/2026-05-13-ai-disclosure-schema-discovery.md` §4.3-4.6
+- Renderer protocol (consumer): `policy_anchor_disclosure_protocol.md` (forthcoming in this branch)
+- v3.2 venue policy database (Nature de-dup peer): `venue_disclosure_policies.md`
+- v3.2 disclosure mode protocol (extension target): `disclosure_mode_protocol.md`
+- Shared Nature policy source (canonical pointer, forthcoming): `shared/policy_data/nature_policy.md`