psyclaw 0.27.22 → 0.28.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1048) hide show
  1. package/README.md +11 -5
  2. package/dist/apps/panel/index.html +2 -2
  3. package/dist/src/adapters/pi/extension.js +225 -92
  4. package/dist/src/adapters/pi/extension.js.map +1 -1
  5. package/dist/src/agents/import.js +44 -32
  6. package/dist/src/agents/import.js.map +1 -1
  7. package/dist/src/analysis/hooks.d.ts +1 -0
  8. package/dist/src/analysis/hooks.js +20 -1
  9. package/dist/src/analysis/hooks.js.map +1 -1
  10. package/dist/src/ars/bridge.d.ts +20 -0
  11. package/dist/src/ars/bridge.js +132 -0
  12. package/dist/src/ars/bridge.js.map +1 -0
  13. package/dist/src/ars/contracts.d.ts +55 -0
  14. package/dist/src/ars/contracts.js +2 -0
  15. package/dist/src/ars/contracts.js.map +1 -0
  16. package/dist/src/ars/panel-plan.d.ts +4 -0
  17. package/dist/src/ars/panel-plan.js +11 -0
  18. package/dist/src/ars/panel-plan.js.map +1 -0
  19. package/dist/src/ars/pi-panel-executor.d.ts +30 -0
  20. package/dist/src/ars/pi-panel-executor.js +140 -0
  21. package/dist/src/ars/pi-panel-executor.js.map +1 -0
  22. package/dist/src/ars/profile.d.ts +36 -0
  23. package/dist/src/ars/profile.js +119 -0
  24. package/dist/src/ars/profile.js.map +1 -0
  25. package/dist/src/ars/re-review.d.ts +22 -0
  26. package/dist/src/ars/re-review.js +172 -0
  27. package/dist/src/ars/re-review.js.map +1 -0
  28. package/dist/src/branding.d.ts +2 -4
  29. package/dist/src/branding.js +3 -5
  30. package/dist/src/branding.js.map +1 -1
  31. package/dist/src/bundled-tools.d.ts +3 -0
  32. package/dist/src/bundled-tools.js +21 -0
  33. package/dist/src/bundled-tools.js.map +1 -0
  34. package/dist/src/chat.js +6 -5
  35. package/dist/src/chat.js.map +1 -1
  36. package/dist/src/creation/contracts.d.ts +38 -0
  37. package/dist/src/creation/contracts.js +2 -0
  38. package/dist/src/creation/contracts.js.map +1 -0
  39. package/dist/src/creation/service.d.ts +7 -0
  40. package/dist/src/creation/service.js +196 -0
  41. package/dist/src/creation/service.js.map +1 -0
  42. package/dist/src/index.d.ts +10 -0
  43. package/dist/src/index.js +10 -0
  44. package/dist/src/index.js.map +1 -1
  45. package/dist/src/install/installer.js +32 -10
  46. package/dist/src/install/installer.js.map +1 -1
  47. package/dist/src/orchestration/personas.d.ts +15 -0
  48. package/dist/src/orchestration/personas.js +51 -0
  49. package/dist/src/orchestration/personas.js.map +1 -0
  50. package/dist/src/orchestration/pi-executor.d.ts +1 -0
  51. package/dist/src/orchestration/pi-executor.js +1 -1
  52. package/dist/src/orchestration/pi-executor.js.map +1 -1
  53. package/dist/src/panel/extension.js +29 -8
  54. package/dist/src/panel/extension.js.map +1 -1
  55. package/dist/src/panel/server.js +14 -5
  56. package/dist/src/panel/server.js.map +1 -1
  57. package/dist/src/project/paths.d.ts +3 -0
  58. package/dist/src/project/paths.js +7 -0
  59. package/dist/src/project/paths.js.map +1 -1
  60. package/dist/src/rules/user-rules.d.ts +8 -0
  61. package/dist/src/rules/user-rules.js +36 -0
  62. package/dist/src/rules/user-rules.js.map +1 -0
  63. package/dist/src/skills/contracts.d.ts +4 -4
  64. package/dist/src/skills/recommended.js +1 -1
  65. package/dist/src/skills/registry.js +49 -28
  66. package/dist/src/skills/registry.js.map +1 -1
  67. package/dist/src/style/cli-ui.js +0 -1
  68. package/dist/src/style/cli-ui.js.map +1 -1
  69. package/package.json +14 -3
  70. package/scripts/rebrand-pi.mjs +6 -0
  71. package/skills/recommended/catalog.json +2 -11
  72. package/vendor/ars/.claude/CLAUDE.md +371 -0
  73. package/vendor/ars/.command-invariants.toml +24 -0
  74. package/vendor/ars/CITATION.cff +35 -0
  75. package/vendor/ars/LICENSE +417 -0
  76. package/vendor/ars/MODE_REGISTRY.md +76 -0
  77. package/vendor/ars/NOTICE.md +26 -0
  78. package/vendor/ars/POSITIONING.md +99 -0
  79. package/vendor/ars/PSYCLAW_SOURCE.json +10 -0
  80. package/vendor/ars/README.md +751 -0
  81. package/vendor/ars/SECURITY.md +52 -0
  82. package/vendor/ars/THIRD_PARTY.md +70 -0
  83. package/vendor/ars/academic-paper/SKILL.md +542 -0
  84. package/vendor/ars/academic-paper/agents/abstract_bilingual_agent.md +171 -0
  85. package/vendor/ars/academic-paper/agents/argument_builder_agent.md +276 -0
  86. package/vendor/ars/academic-paper/agents/citation_compliance_agent.md +422 -0
  87. package/vendor/ars/academic-paper/agents/draft_writer_agent.md +656 -0
  88. package/vendor/ars/academic-paper/agents/formatter_agent.md +999 -0
  89. package/vendor/ars/academic-paper/agents/intake_agent.md +393 -0
  90. package/vendor/ars/academic-paper/agents/literature_strategist_agent.md +626 -0
  91. package/vendor/ars/academic-paper/agents/peer_reviewer_agent.md +516 -0
  92. package/vendor/ars/academic-paper/agents/revision_coach_agent.md +334 -0
  93. package/vendor/ars/academic-paper/agents/socratic_mentor_agent.md +527 -0
  94. package/vendor/ars/academic-paper/agents/structure_architect_agent.md +401 -0
  95. package/vendor/ars/academic-paper/agents/visualization_agent.md +441 -0
  96. package/vendor/ars/academic-paper/examples/chinese_paper_example.md +278 -0
  97. package/vendor/ars/academic-paper/examples/clinical_citation_verification_checklist.md +95 -0
  98. package/vendor/ars/academic-paper/examples/clinical_epistemic_status_example.md +100 -0
  99. package/vendor/ars/academic-paper/examples/commitment_ledger_example.md +147 -0
  100. package/vendor/ars/academic-paper/examples/imrad_hei_example.md +234 -0
  101. package/vendor/ars/academic-paper/examples/literature_review_example.md +260 -0
  102. package/vendor/ars/academic-paper/examples/plan_mode_guided_writing.md +600 -0
  103. package/vendor/ars/academic-paper/examples/revision_mode_example.md +344 -0
  104. package/vendor/ars/academic-paper/examples/revision_recovery_example.md +506 -0
  105. package/vendor/ars/academic-paper/examples/version_family_reconciliation_example.md +89 -0
  106. package/vendor/ars/academic-paper/references/abstract_writing_guide.md +169 -0
  107. package/vendor/ars/academic-paper/references/academic_writing_style.md +188 -0
  108. package/vendor/ars/academic-paper/references/anti_leakage_protocol.md +83 -0
  109. package/vendor/ars/academic-paper/references/apa7_chinese_citation_guide.md +364 -0
  110. package/vendor/ars/academic-paper/references/apa7_extended_guide.md +198 -0
  111. package/vendor/ars/academic-paper/references/changelog.md +11 -0
  112. package/vendor/ars/academic-paper/references/citation_format_switcher.md +228 -0
  113. package/vendor/ars/academic-paper/references/committee_correspondence_protocol.md +158 -0
  114. package/vendor/ars/academic-paper/references/credit_authorship_guide.md +308 -0
  115. package/vendor/ars/academic-paper/references/disclosure_mode_protocol.md +478 -0
  116. package/vendor/ars/academic-paper/references/domain_evidence_profiles.md +38 -0
  117. package/vendor/ars/academic-paper/references/failure_paths.md +349 -0
  118. package/vendor/ars/academic-paper/references/funding_statement_guide.md +319 -0
  119. package/vendor/ars/academic-paper/references/hei_domain_glossary.md +169 -0
  120. package/vendor/ars/academic-paper/references/intro_title_rhetoric_guide.md +114 -0
  121. package/vendor/ars/academic-paper/references/journal_submission_guide.md +249 -0
  122. package/vendor/ars/academic-paper/references/latex_template_reference.md +378 -0
  123. package/vendor/ars/academic-paper/references/mode_selection_guide.md +378 -0
  124. package/vendor/ars/academic-paper/references/paper_structure_patterns.md +330 -0
  125. package/vendor/ars/academic-paper/references/plan_mode_protocol.md +112 -0
  126. package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md +200 -0
  127. package/vendor/ars/academic-paper/references/policy_anchor_table.md +157 -0
  128. package/vendor/ars/academic-paper/references/revision_patch_protocol.md +173 -0
  129. package/vendor/ars/academic-paper/references/statistical_visualization_standards.md +750 -0
  130. package/vendor/ars/academic-paper/references/venue_disclosure_policies.md +259 -0
  131. package/vendor/ars/academic-paper/references/vlm_figure_verification.md +126 -0
  132. package/vendor/ars/academic-paper/references/workflow_phase_details.md +135 -0
  133. package/vendor/ars/academic-paper/references/writing_judgment_framework.md +59 -0
  134. package/vendor/ars/academic-paper/references/writing_quality_check.md +173 -0
  135. package/vendor/ars/academic-paper/templates/bilingual_abstract_template.md +78 -0
  136. package/vendor/ars/academic-paper/templates/case_study_template.md +129 -0
  137. package/vendor/ars/academic-paper/templates/conference_paper_template.md +108 -0
  138. package/vendor/ars/academic-paper/templates/credit_statement_template.md +132 -0
  139. package/vendor/ars/academic-paper/templates/funding_statement_template.md +290 -0
  140. package/vendor/ars/academic-paper/templates/imrad_template.md +183 -0
  141. package/vendor/ars/academic-paper/templates/latex_article_template.tex +199 -0
  142. package/vendor/ars/academic-paper/templates/literature_review_template.md +135 -0
  143. package/vendor/ars/academic-paper/templates/policy_brief_template.md +139 -0
  144. package/vendor/ars/academic-paper/templates/revision_tracking_template.md +199 -0
  145. package/vendor/ars/academic-paper/templates/theoretical_paper_template.md +119 -0
  146. package/vendor/ars/academic-paper-reviewer/SKILL.md +491 -0
  147. package/vendor/ars/academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md +443 -0
  148. package/vendor/ars/academic-paper-reviewer/agents/domain_reviewer_agent.md +412 -0
  149. package/vendor/ars/academic-paper-reviewer/agents/editorial_synthesizer_agent.md +478 -0
  150. package/vendor/ars/academic-paper-reviewer/agents/eic_agent.md +339 -0
  151. package/vendor/ars/academic-paper-reviewer/agents/field_analyst_agent.md +221 -0
  152. package/vendor/ars/academic-paper-reviewer/agents/methodology_reviewer_agent.md +449 -0
  153. package/vendor/ars/academic-paper-reviewer/agents/perspective_reviewer_agent.md +427 -0
  154. package/vendor/ars/academic-paper-reviewer/examples/hei_paper_review_example.md +391 -0
  155. package/vendor/ars/academic-paper-reviewer/examples/interdisciplinary_review_example.md +299 -0
  156. package/vendor/ars/academic-paper-reviewer/examples/subclaim_decomposition_example.md +80 -0
  157. package/vendor/ars/academic-paper-reviewer/references/calibration_mode_protocol.md +256 -0
  158. package/vendor/ars/academic-paper-reviewer/references/changelog.md +10 -0
  159. package/vendor/ars/academic-paper-reviewer/references/editorial_decision_standards.md +236 -0
  160. package/vendor/ars/academic-paper-reviewer/references/guided_mode_protocol.md +34 -0
  161. package/vendor/ars/academic-paper-reviewer/references/integration_guide.md +15 -0
  162. package/vendor/ars/academic-paper-reviewer/references/quality_rubrics.md +84 -0
  163. package/vendor/ars/academic-paper-reviewer/references/re_review_mode_protocol.md +340 -0
  164. package/vendor/ars/academic-paper-reviewer/references/review_criteria_framework.md +98 -0
  165. package/vendor/ars/academic-paper-reviewer/references/review_panel_provenance_protocol.md +197 -0
  166. package/vendor/ars/academic-paper-reviewer/references/review_quality_thinking.md +58 -0
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  169. package/vendor/ars/academic-paper-reviewer/references/statistical_reporting_standards.md +505 -0
  170. package/vendor/ars/academic-paper-reviewer/references/top_journals_by_field.md +206 -0
  171. package/vendor/ars/academic-paper-reviewer/templates/editorial_decision_template.md +235 -0
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  175. package/vendor/ars/academic-pipeline/agents/claim_ref_alignment_audit_agent.md +382 -0
  176. package/vendor/ars/academic-pipeline/agents/collaboration_depth_agent.md +164 -0
  177. package/vendor/ars/academic-pipeline/agents/integrity_verification_agent.md +870 -0
  178. package/vendor/ars/academic-pipeline/agents/pipeline_orchestrator_agent.md +1379 -0
  179. package/vendor/ars/academic-pipeline/agents/state_tracker_agent.md +622 -0
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  181. package/vendor/ars/academic-pipeline/examples/integrity_failure_recovery.md +389 -0
  182. package/vendor/ars/academic-pipeline/examples/mid_entry_example.md +414 -0
  183. package/vendor/ars/academic-pipeline/references/adapters/.gitkeep +0 -0
  184. package/vendor/ars/academic-pipeline/references/adapters/overview.md +153 -0
  185. package/vendor/ars/academic-pipeline/references/ai_research_failure_modes.md +185 -0
  186. package/vendor/ars/academic-pipeline/references/changelog.md +14 -0
  187. package/vendor/ars/academic-pipeline/references/claim_audit_calibration_protocol.md +175 -0
  188. package/vendor/ars/academic-pipeline/references/claim_verification_protocol.md +282 -0
  189. package/vendor/ars/academic-pipeline/references/external_review_protocol.md +131 -0
  190. package/vendor/ars/academic-pipeline/references/integrity_review_protocol.md +110 -0
  191. package/vendor/ars/academic-pipeline/references/literature_corpus_consumers.md +193 -0
  192. package/vendor/ars/academic-pipeline/references/mode_advisor.md +135 -0
  193. package/vendor/ars/academic-pipeline/references/passport_as_reset_boundary.md +132 -0
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  204. package/vendor/ars/agents/report_compiler_agent.md +341 -0
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  207. package/vendor/ars/commands/ars-3w.md +10 -0
  208. package/vendor/ars/commands/ars-abstract.md +10 -0
  209. package/vendor/ars/commands/ars-cache-invalidate.md +20 -0
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  213. package/vendor/ars/commands/ars-full.md +9 -0
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@@ -0,0 +1,136 @@
1
+ ---
2
+ name: compliance_agent
3
+ description: "Runs PRISMA-trAIce + RAISE compliance checks at Stage 2.5 / 4.5 integrity gates and emits Schema 12 compliance_report"
4
+ version: 1.0.0
5
+ owner_skill: shared
6
+ invoked_by: [academic-pipeline, deep-research, academic-paper]
7
+ data_access_level: verified_only
8
+ task_type: open-ended
9
+ status: active
10
+ related_skills: [academic-pipeline, deep-research, academic-paper]
11
+ last_updated: "2026-04-20"
12
+ related_protocols:
13
+ - shared/prisma_trAIce_protocol.md
14
+ - shared/raise_framework.md
15
+ - shared/compliance_checkpoint_protocol.md
16
+ - shared/compliance_report.schema.json
17
+ - academic-paper/references/anti_leakage_protocol.md
18
+ - academic-pipeline/references/ai_research_failure_modes.md
19
+ ---
20
+
21
+ # compliance_agent
22
+
23
+ Mode-aware agent that runs PRISMA-trAIce + RAISE compliance checks at Stage 2.5 / 4.5 Integrity Gates, producing Schema 12 `compliance_report` outputs.
24
+
25
+ ## Scope
26
+
27
+ - **Reads:** manuscript draft, methodology blueprint, bibliography, material passport, user-provided AI tool metadata
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+ - **Writes nothing to the manuscript.** Output is a separate `compliance_report` handed to the orchestrator.
29
+ - **Does not hallucinate missing items.** Anti-Leakage Protocol applies: missing material → `[MATERIAL GAP: <item_id>]` in the gap reason (see [`shared/compliance_checkpoint_protocol.md#canonical-gap-tag-vocabulary`](../compliance_checkpoint_protocol.md#canonical-gap-tag-vocabulary)).
30
+
31
+ ## Input contract
32
+
33
+ ```yaml
34
+ compliance_mode: "systematic_review" | "primary_research" | "other_evidence_synthesis"
35
+ stage: "2.5" | "4.5"
36
+ materials:
37
+ manuscript_draft: <path or inline>
38
+ methodology_blueprint: <path>
39
+ bibliography: <path>
40
+ material_passport: <Schema 9 payload>
41
+ user_metadata:
42
+ intended_venue: <string or null>
43
+ ai_tools_used:
44
+ - {name, version, developer, stage, purpose, access_url_or_doi}
45
+ ```
46
+
47
+ ## Output contract
48
+
49
+ `compliance_report` conforming to `shared/compliance_report.schema.json` (Schema 12). Appended to `material_passport.compliance_history[]` by the orchestrator.
50
+
51
+ ## Dispatch logic
52
+
53
+ ```python
54
+ if compliance_mode == "systematic_review":
55
+ run PRISMA-trAIce checks (Stage-specific item subset)
56
+ run RAISE full (principles + 8-role matrix)
57
+ block_decision respects tier semantics
58
+ elif compliance_mode == "other_evidence_synthesis":
59
+ run PRISMA-trAIce checks in "adaptation" mode (items become Info)
60
+ run RAISE full
61
+ block_decision capped at warn
62
+ elif compliance_mode == "primary_research":
63
+ run RAISE principles_only
64
+ set prisma_trAIce to null
65
+ block_decision capped at warn
66
+ ```
67
+
68
+ ## Stage behaviour
69
+
70
+ | Stage | PRISMA-trAIce items checked | RAISE focus |
71
+ |---|---|---|
72
+ | 2.5 | M1, M2, M3, M4, M5, M6, M7, M8, M9, M10 | human_oversight, fit_for_purpose |
73
+ | 4.5 | T1, A1, I1, R1, R2, D1, D2 | transparency, reproducibility (+ full 8-role matrix for SR) |
74
+
75
+ Items within each stage subset are independent and MAY be evaluated concurrently. The agent SHOULD read `material_passport.compliance_history[]` only for prior-loop auditability context; prior reports are not re-evaluated.
76
+
77
+ ## Tier → decision mapping (SR mode)
78
+
79
+ | Tier | FAIL → |
80
+ |---|---|
81
+ | Mandatory | `block_decision = block` |
82
+ | Highly Recommended | `block_decision = warn` |
83
+ | Recommended | `block_decision = pass` (logged as info) |
84
+ | Optional | `block_decision = pass` (logged as info) |
85
+
86
+ Multiple tier contributions aggregate using `max_severity` (see `compliance_checkpoint_protocol.md §Decision precedence`).
87
+
88
+ ### Mandatory-block surface message
89
+
90
+ When a Mandatory-tier PRISMA-trAIce item triggers `block_decision = block`, the surfaced block message MUST include the following maturity note alongside the gap reason and override-ladder reference, so the user understands what authority is blocking them:
91
+
92
+ > *Note: PRISMA-trAIce is currently a foundational proposal (Holst et al. 2025, *JMIR AI*, doi:[10.2196/80247](https://doi.org/10.2196/80247)), developed via systematic adaptation rather than a formal Delphi consensus study. Items have not yet been empirically validated across diverse research contexts. See `shared/prisma_trAIce_protocol.md` § Status disclaimer.*
93
+
94
+ This note is informational only — it does not lower the block severity. The Mandatory-as-block design choice follows the authors' own argument (Holst et al. 2025) that non-transparent AI use is the higher-cost failure mode. Surfacing the maturity note mirrors the disclosure pattern in [`academic-pipeline/references/plagiarism_detection_protocol.md`](../../academic-pipeline/references/plagiarism_detection_protocol.md), which discloses heuristic-screening scope to the user.
95
+
96
+ ## Self-check protocol
97
+
98
+ Before finalising the report, the agent runs four self-checks. Any flagged check requires re-examination:
99
+
100
+ | ID | Question | On fail |
101
+ |---|---|---|
102
+ | CA-1 | Am I quoting PRISMA-trAIce items from memory or from `shared/prisma_trAIce_protocol.md`? | Re-read the protocol file; requote. |
103
+ | CA-2 | Are my block decisions anchored to each item's stated tier, not promoted/demoted from memory? | Re-read tier assignments; correct any drift. |
104
+ | CA-3 | **SR mode only.** Did all 17 items pass AND `evidence[]` is empty? (Sycophancy risk) | Do a second pass over the 3 most-commonly-missed Mandatory items (M4, M6, M8); require explicit evidence path citation. |
105
+ | CA-4 | For each RAISE principle marked `pass`, is `principle_evidence[<principle>]` non-empty? | Downgrade the principle to `warn` with note `[WEAK EVIDENCE]`. |
106
+
107
+ Self-check failures are not errors — they are the agent's guardrail. Document the self-check pass/fail in the agent log (not in compliance_report) for auditability.
108
+
109
+ ## Error behaviour
110
+
111
+ | Error | Handling |
112
+ |---|---|
113
+ | Missing input material | Apply Anti-Leakage: mark `[MATERIAL GAP]`, item auto-FAILs, tier dictates block/warn. Never hallucinate. |
114
+ | Mode/context mismatch (e.g. `academic-paper full` passes SR mode) | Refuse with `{decision: "abort", reason: "mode/context mismatch"}`. Orchestrator must re-evaluate and re-invoke. |
115
+ | Schema validation failure on own output | Halt, surface internal error to orchestrator. Do NOT append invalid report to compliance_history. |
116
+ | Upstream drift (snapshot_date vs GitHub) | Set `upstream_sync_status: "stale"` in report. Non-blocking. |
117
+
118
+ <!-- harness-retirement 2026-06-10 (F-008): the "Never hallucinate." tail on the missing-input row is kept as known debt — high-stakes academic compliance surface with a silent failure mode; delete only with calibration evidence that the tail is inert. -->
119
+
120
+ ## Interaction with existing agents
121
+
122
+ - Runs AFTER `integrity_verification_agent` (existing) at Stage 2.5 / 4.5 — compliance extends integrity, does not replace it.
123
+ - Runs ALONGSIDE `failure_mode_checklist` (v3.2). Non-overlapping scope: failure_mode checks research validity; compliance checks reporting transparency.
124
+ - Provides output consumed by `report_compiler_agent` (at Stage 6) for the AI Self-Reflection Report compliance summary.
125
+
126
+ ## Invocation protocol
127
+
128
+ The orchestrator (or standalone skill) passes the input contract via the Agent tool with `model: sonnet` or higher (per user CLAUDE.md: never haiku). The agent returns the serialised compliance_report. The orchestrator validates against Schema 12 before appending to passport.
129
+
130
+ ## Related reading
131
+
132
+ - `shared/prisma_trAIce_protocol.md` — item-level checks
133
+ - `shared/raise_framework.md` — principle definitions and role matrix
134
+ - `shared/compliance_checkpoint_protocol.md` — checkpoint behaviour and override ladder
135
+ - `academic-paper/references/anti_leakage_protocol.md` — gap-marking discipline
136
+ - `academic-pipeline/references/pipeline_state_machine.md` — FAIL-loop integration
@@ -0,0 +1,173 @@
1
+ # Artifact Reproducibility Pattern (v3.3.5+)
2
+
3
+ ## Why this exists
4
+
5
+ ARS produces research artifacts — draft papers, literature reviews, review reports. A year
6
+ from now, you may want to reproduce one. Today's Material Passport (Schema 9) captures WHO
7
+ produced the artifact and WHEN, but not WITH WHAT. Which LLM? Which ARS version? Which
8
+ skill files? Which session materials?
9
+
10
+ The `repro_lock` sub-block fills that gap.
11
+
12
+ When the Anthropic automated-w2s-researcher paper (2026) claimed "2 researchers × 7 days
13
+ vs 9 agents × 5 days," readers had no way to audit the conditions. This pattern ensures
14
+ that ARS-produced artifacts carry their configuration on record — not as a replay mechanism,
15
+ but as an honest documentation trail.
16
+
17
+ ## What this pattern IS NOT (read this first)
18
+
19
+ This is non-negotiable. Every future user MUST read this section before assuming the lock
20
+ guarantees anything it does not.
21
+
22
+ 1. **LLM outputs are not byte-reproducible even at temperature 0.** Model providers update
23
+ weights without changing the model id. `model.weight_stable: false` acknowledges this
24
+ explicitly. `model.id` is an identifier, not a weight hash.
25
+
26
+ 2. **Live external API queries are recorded as protocol versions, not snapshots.** The S2
27
+ API changes daily. A paper citing DOI 10.1000/x today may return different metadata
28
+ tomorrow. `s2_api_protocol_version` records which VERSION of our query logic ran, not
29
+ a snapshot of the response.
30
+
31
+ 3. **Mid-skill prompt mutations are not captured.** `prompts.hash_timing: "skill-load"` is
32
+ a declaration: hashes are taken when the skill loads, not per agent call. Late injection
33
+ of user-provided reference files, conditional branches, and dynamic prompt modifications
34
+ are NOT reflected in the hash. This is a known imprecision.
35
+
36
+ 4. **`stochasticity_declaration` is required, not optional.** Omitting it makes the lock
37
+ dishonest by implication. Every generated passport includes the declaration verbatim.
38
+
39
+ If you want deterministic replay, you are reading the wrong pattern. This pattern gives
40
+ you CONFIGURATION DOCUMENTATION sufficient to INVESTIGATE divergence — not to PREVENT it.
41
+
42
+ ## The block at a glance
43
+
44
+ ```yaml
45
+ repro_lock:
46
+ schema_version: "1.0" # lock schema version
47
+ stochasticity_declaration: "LLM outputs are not byte-reproducible. This lockfile documents configuration, not a deterministic replay guarantee."
48
+ ars_version: "<suite-version-at-run-time>" # e.g. "3.11.1" — the suite version when this run executed
49
+
50
+ model:
51
+ family: claude # provider family
52
+ id: "<model-id-at-run-time>" # model identifier at run time, e.g. the inherited Claude Code session model (not weight hash)
53
+ weight_stable: false # always false until signed attestation exists
54
+
55
+ prompts:
56
+ hash_timing: skill-load # when hashes were taken
57
+ skill_md_hash: "sha256:..." # hash of the skill SKILL.md file
58
+ agents_bundle_hash: "sha256:..." # hash of agent prompt bundle
59
+
60
+ materials:
61
+ list_hash: "sha256:..." # hash of [{filename, sha256}, ...] manifest
62
+ count: 8 # number of session materials
63
+
64
+ external_protocols:
65
+ s2_api_protocol_version: "<s2-protocol-version-at-run-time>" # the S2 query protocol version that ran
66
+ s2_snapshot_available: false # whether a response cache exists
67
+
68
+ cross_model:
69
+ enabled: false # whether cross-model verification ran
70
+ secondary_model_id: null # secondary model id if enabled
71
+ ```
72
+
73
+ The block lives as an optional child of the Material Passport (Schema 9 in
74
+ `shared/handoff_schemas.md`). A missing key fails the lint. A null value passes with a
75
+ warning. A populated block with all required sub-fields passes silently.
76
+
77
+ ## Field-by-field rationale
78
+
79
+ ### schema_version
80
+
81
+ `"1.0"` currently supported. Schema evolution policy: breaking changes bump major,
82
+ additions bump minor. Old readers fail loudly on unknown versions — `check_repro_lock.py`
83
+ will exit 1 if it encounters an unrecognized version, forcing the user to upgrade their
84
+ tooling or audit the change manually.
85
+
86
+ ### ars_version
87
+
88
+ Suite version from CHANGELOG. This couples the prompt hashes to the release: changing
89
+ `ars_version` will change the bundle hash even if individual prompt files didn't change.
90
+ That coupling is intentional — version boundaries mark coordinated changes.
91
+
92
+ ### model.weight_stable
93
+
94
+ Currently always `false`. Reserved for a future world where a provider guarantees weight
95
+ stability with a signed attestation. Not today. If you see `true`, treat it as suspicious
96
+ until a signed attestation mechanism exists.
97
+
98
+ ### prompts.hash_timing
99
+
100
+ Fixed at `"skill-load"` in v1.0. A future `"per-call"` variant would require runtime
101
+ instrumentation not present today. The spec is left open for future work. For now, the
102
+ hash captures the state of files at skill initialization, not at every agent invocation.
103
+
104
+ ### materials.list_hash
105
+
106
+ Hash of a sorted manifest: `[{filename, sha256}, ...]` sorted by filename. If the user
107
+ edits a session material between runs, the hash changes — which is the correct behavior.
108
+ An identical hash across two runs means the input materials were identical; different
109
+ hashes mean inputs diverged.
110
+
111
+ ### external_protocols.s2_snapshot_available
112
+
113
+ Almost always `false` today. If a future version of the pipeline caches S2 responses per
114
+ run and stores them alongside the passport, this flag flips to `true` and the snapshot path
115
+ appears in the passport. Until that exists, S2 responses are live queries and are not
116
+ reproducible.
117
+
118
+ ## How it composes with existing infrastructure
119
+
120
+ - Material Passport (Schema 9) is the PARENT document. `repro_lock` is an OPTIONAL CHILD
121
+ field. A passport without `repro_lock` fails the v3.3.5+ lint; a passport with
122
+ `repro_lock: null` passes with a warning (explicit opt-out).
123
+ - Existing passports with `repro_lock` absent fail the new lint. Existing passports with
124
+ `repro_lock: null` pass with a warning. Populated blocks pass silently.
125
+ - The integrity gate (Stage 2.5, Stage 4.5 in the academic pipeline) does NOT read
126
+ `repro_lock`. The lock is for post-hoc reproducibility investigation, not runtime
127
+ validation. Adding it does not change pipeline behavior.
128
+ - `check_repro_lock.py` can be run standalone on any passport file. It is not wired into
129
+ the CI lint suite by default — it validates on-demand against specific passport files.
130
+
131
+ ## Red flags when reading a populated repro_lock
132
+
133
+ - `model.weight_stable: true` — this value is not implemented yet; if you see it, the
134
+ passport author is claiming something the infrastructure cannot verify. Treat as
135
+ suspicious until a signed attestation mechanism exists.
136
+ - `prompts.hash_timing` anything other than `"skill-load"` — this is an unknown variant
137
+ that the current tooling does not understand. The lint will not flag it as invalid, but
138
+ the semantics are undefined.
139
+ - Empty or stub hashes (`"sha256:"` prefix with no content, or a short placeholder string
140
+ like `"sha256:abc123"`) — the generator was broken or the author filled in a placeholder.
141
+ Hashes should be 64-character hex strings for SHA-256.
142
+ - `stochasticity_declaration` modified from the verbatim required string — the author is
143
+ signalling they believe the lock is stronger than it is. Read the entire passport twice
144
+ before trusting any claims about reproducibility.
145
+
146
+ ## How to generate a lock (for agent authors)
147
+
148
+ At skill-load time, compute `skill_md_hash` over the SKILL.md content and
149
+ `agents_bundle_hash` over the concatenated agent prompts (canonical ordering). Build the
150
+ materials manifest by listing session files with their SHA-256 digests, sort by filename,
151
+ then hash the JSON serialization. Write the block to the passport before handing off to
152
+ downstream stages. The `stochasticity_declaration` must be included verbatim — do not
153
+ paraphrase or abbreviate it.
154
+
155
+ ## Honesty red line (restate)
156
+
157
+ This pattern enables HONEST DOCUMENTATION. It does not enable REPLAY. Every field has a
158
+ reason and a limitation. Users who treat the lock as a replay guarantee will be burned.
159
+ Authors who publish passports without `stochasticity_declaration` are failing their readers.
160
+ The locked configuration tells you what ran; it cannot tell you what would run again.
161
+
162
+ The distinction matters: documentation lets a third party investigate what happened and
163
+ ask whether divergence is expected or alarming. Replay would require weight-frozen models,
164
+ deterministic schedulers, and cached external data — none of which ARS controls today.
165
+
166
+ ## Future evolution
167
+
168
+ - v1.1: add `cache_snapshot_available: true` support once the pipeline caches S2 responses.
169
+ The snapshot path would appear as a sibling field in `external_protocols`.
170
+ - v2.0: if weight-signed attestations exist, `model.weight_stable: true` becomes meaningful.
171
+ Until then the field is reserved.
172
+ - Never: byte-level replay guarantees. LLMs don't work like that; no schema version will
173
+ change that fact.
@@ -0,0 +1,81 @@
1
+ {
2
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
3
+ "$id": "https://github.com/Imbad0202/academic-research-skills/shared/benchmark_report.schema.json",
4
+ "title": "ARS Benchmark Report",
5
+ "type": "object",
6
+ "required": [
7
+ "ars_version",
8
+ "task_definition",
9
+ "human_baseline",
10
+ "ars_run",
11
+ "metrics",
12
+ "caveats"
13
+ ],
14
+ "properties": {
15
+ "ars_version": {
16
+ "type": "string",
17
+ "pattern": "^\\d+\\.\\d+\\.\\d+$",
18
+ "description": "Exact ARS version the benchmark was run against"
19
+ },
20
+ "task_definition": {
21
+ "type": "object",
22
+ "required": ["description", "task_type", "outcome_gradable"],
23
+ "properties": {
24
+ "description": { "type": "string", "minLength": 1 },
25
+ "task_type": { "enum": ["outcome-gradable", "open-ended"] },
26
+ "outcome_gradable": { "type": "boolean" }
27
+ }
28
+ },
29
+ "human_baseline": {
30
+ "type": "object",
31
+ "required": ["sample_size", "author_independence", "hours_spent", "recruitment", "tools_allowed"],
32
+ "properties": {
33
+ "sample_size": { "type": "integer", "minimum": 1 },
34
+ "author_independence": {
35
+ "enum": ["author-conducted", "author-blinded", "third-party-conducted"],
36
+ "description": "author-conducted means the benchmark creators also did the human baseline (downward bias risk)"
37
+ },
38
+ "hours_spent": { "type": "number", "minimum": 0 },
39
+ "recruitment": { "type": "string", "minLength": 1 },
40
+ "tools_allowed": {
41
+ "type": "array",
42
+ "items": { "type": "string", "minLength": 1 },
43
+ "minItems": 1
44
+ }
45
+ }
46
+ },
47
+ "ars_run": {
48
+ "type": "object",
49
+ "required": ["hours_spent", "cost_usd", "skills_used", "data_access_level_declared"],
50
+ "properties": {
51
+ "hours_spent": { "type": "number", "minimum": 0 },
52
+ "cost_usd": { "type": "number", "minimum": 0 },
53
+ "skills_used": {
54
+ "type": "array",
55
+ "items": { "type": "string" },
56
+ "minItems": 1
57
+ },
58
+ "data_access_level_declared": {
59
+ "enum": ["raw", "redacted", "verified_only"]
60
+ }
61
+ }
62
+ },
63
+ "metrics": {
64
+ "type": "object",
65
+ "required": ["primary_metric", "primary_metric_value", "scoring_independence"],
66
+ "properties": {
67
+ "primary_metric": { "type": "string", "minLength": 1 },
68
+ "primary_metric_value": { "type": "number" },
69
+ "scoring_independence": {
70
+ "enum": ["authors-scored", "third-party-scored", "blind-scored", "self-scored"]
71
+ }
72
+ }
73
+ },
74
+ "caveats": {
75
+ "type": "array",
76
+ "items": { "type": "string", "minLength": 1 },
77
+ "minItems": 1,
78
+ "description": "Known limitations. Empty array not permitted — honest disclosure required."
79
+ }
80
+ }
81
+ }
@@ -0,0 +1,180 @@
1
+ # Benchmark Report Pattern (v3.3.5+)
2
+
3
+ **Status**: v3.3.5 — hub doc for benchmark disclosure schema
4
+ **Schema**: `shared/benchmark_report.schema.json`
5
+ **Validator**: `scripts/check_benchmark_report.py`
6
+ **Template**: `examples/benchmark_report_template.json`
7
+
8
+ ---
9
+
10
+ ## Why this exists
11
+
12
+ The Anthropic automated-w2s-researcher (2026) paper headlined a performance comparison:
13
+ "2 researchers × 7 days (PGR=0.23) vs 9 agents × 5 days (PGR=0.97)."
14
+
15
+ Dramatic. Also: n=2, author-conducted, no independence, self-scored. Not a scientific
16
+ comparison — a presentation artifact. The authors knew what the agent would produce before
17
+ sitting down to do the human baseline; their "7 days" is implicitly benchmarked against
18
+ their own foreknowledge. Unaware external researchers doing the same task cold would
19
+ likely score higher. The gap may partly be a sandbagged human baseline.
20
+
21
+ ARS inherits this risk the moment a user publishes an "ARS beats manual" claim. This
22
+ pattern defines a mandatory schema for anyone publishing an ARS benchmark comparison.
23
+ Reports that don't satisfy the schema aren't "ARS benchmarks" — they're anecdotes.
24
+
25
+ ---
26
+
27
+ ## The schema at a glance
28
+
29
+ Six required top-level fields in `benchmark_report.schema.json`:
30
+
31
+ - **`ars_version`** — exact semver the benchmark ran against; ties results to a specific
32
+ skill version so readers can check whether that version is still current.
33
+ - **`task_definition`** — description, task_type (outcome-gradable or open-ended), and
34
+ outcome_gradable flag; distinguishes rubric-scored tasks from genuinely open-ended ones.
35
+ - **`human_baseline`** — the five provenance fields that determine whether the human side
36
+ of the comparison is credible (see field-by-field rationale below).
37
+ - **`ars_run`** — cost, time, skills used, and declared data access level; lets readers
38
+ check the "agents are cheap" or "agents are fast" claims against concrete numbers.
39
+ - **`metrics`** — primary metric name, numeric value, and scoring independence; forces
40
+ explicit disclosure of who scored the outputs.
41
+ - **`caveats`** — non-empty array of known limitations; at least one honest statement is
42
+ required by schema enforcement.
43
+
44
+ ---
45
+
46
+ ## Field-by-field rationale
47
+
48
+ ### `human_baseline`
49
+
50
+ This block exists because the human side of a comparison is where benchmark credibility
51
+ lives or dies. A weak human baseline inflates an agent's apparent advantage.
52
+
53
+ - **`sample_size`** (integer, minimum 1): Schema rejects zero, forces an explicit number.
54
+ n=1 or n=2 get a validator warning rather than a hard failure — some tasks are
55
+ expert-bounded — but the number must be stated. Silence is worse than admitting n=1.
56
+
57
+ - **`author_independence`** (enum: author-conducted | author-blinded | third-party-conducted):
58
+ `author-conducted` is the "2 authors did it themselves" trap: allowed, but the schema
59
+ flags the downward-bias risk. Authors know what a good ARS output looks like; their
60
+ human effort is calibrated against that prior. `author-blinded` (authors worked without
61
+ seeing ARS outputs first) is better. `third-party-conducted` eliminates experimenter
62
+ bias entirely.
63
+
64
+ - **`hours_spent`** (number, minimum 0): Lets third parties sanity-check the time claim.
65
+ "7 days" reads differently against 20 papers versus 400.
66
+
67
+ - **`recruitment`** (non-empty string): One sentence forces self-description of selection
68
+ bias. "Authors," "hired on Upwork," "convenience sample" are all honest. Blank is not
69
+ permitted.
70
+
71
+ - **`tools_allowed`** (array of strings): "No tools" vs "ChatGPT allowed" is not the same
72
+ comparison as ARS. If the human baseline used no AI assistance while ARS ran full
73
+ pipeline, the comparison is testing infrastructure access, not cognitive quality.
74
+
75
+ ### `ars_run`
76
+
77
+ - **`cost_usd`** (number, minimum 0): A run costing $500 in API tokens is not "cheap"
78
+ just because it took 3 hours. Hours and cost together are needed for a fair comparison.
79
+
80
+ - **`data_access_level_declared`** (enum: raw | redacted | verified_only): If ARS ran
81
+ on `raw` data while the human baseline used redacted data, the benchmark is testing
82
+ data privilege, not skill. Cross-references ground-truth isolation from v3.3.2.
83
+
84
+ - **`skills_used`** (array, minItems 1): A benchmark running `academic-pipeline`
85
+ full-mode is not comparable to one running only `deep-research`. Both are ARS;
86
+ they're different scope claims.
87
+
88
+ ### `metrics.scoring_independence`
89
+
90
+ Four enum values: `authors-scored`, `third-party-scored`, `blind-scored`, `self-scored`.
91
+
92
+ `self-scored` parses and exits 0, but the validator emits a warning to stderr. Self-scoring
93
+ is the worst-case alignment failure: the same agents that produced the output are being
94
+ asked whether the output is good. `blind-scored` (human raters without knowledge of which
95
+ output came from ARS versus human baseline) is the minimum credible standard for any
96
+ claim that will be shared publicly.
97
+
98
+ ### `caveats`
99
+
100
+ Non-empty array, items non-empty strings, minItems 1. The schema physically prevents an
101
+ empty caveats field. A benchmark report with no caveats either has no known limitations
102
+ (implausible for any real-world evaluation) or the author didn't think about limitations
103
+ (which disqualifies the report more than any specific limitation would).
104
+
105
+ The caveats field is where sample size warnings, scorer bias, task-selection bias, and
106
+ tool-access asymmetries should land when they don't rise to schema errors. It is the
107
+ honest disclosure box.
108
+
109
+ ---
110
+
111
+ ## How to use
112
+
113
+ 1. Copy `examples/benchmark_report_template.json` to your benchmark directory.
114
+ 2. Fill every `FILL IN:` field with real values.
115
+ 3. Set `human_baseline.sample_size` to the actual number (schema rejects 0).
116
+ 4. Run: `python scripts/check_benchmark_report.py your-report.json`
117
+ 5. Fix all `ERROR:` lines (schema violations, exit 1).
118
+ 6. Read the `WARNING:` lines (stderr, exit 0). Either address them in your methodology or
119
+ document them explicitly in the `caveats` array.
120
+ 7. Publish the JSON file in your repository alongside the benchmark write-up. The
121
+ machine-readable format lets future scripts cross-check version-specific claims.
122
+
123
+ ---
124
+
125
+ ## What this pattern is NOT
126
+
127
+ - **Not a quality gate for your methodology.** A report can be schema-valid and still be
128
+ methodologically weak. The schema forces disclosure; it does not evaluate task choice,
129
+ rubric validity, or baseline skill. Compliance is necessary but not sufficient.
130
+
131
+ - **Not a way to launder self-scored or n=2 comparisons.** `self-scored` and
132
+ `sample_size: 2` produce a valid document. The warnings are loud. Schema compliance
133
+ means the claim is honest about its weaknesses — not that the claim is strong.
134
+
135
+ - **Not a substitute for peer review.** The schema is the minimum bar for internal
136
+ credibility. Peer review catches confounded variables, cherry-picked tasks, post-hoc
137
+ metric selection — problems the schema cannot see.
138
+
139
+ - **Not frozen.** A benchmark declaring `ars_version: 3.3.5` is always checked against
140
+ the v3.3.5 schema. Future versions may add fields without invalidating existing reports.
141
+
142
+ ---
143
+
144
+ ## Honesty red lines
145
+
146
+ These are behaviors the schema is specifically designed to make visible. They are not
147
+ prohibited — the schema accepts all of them — but they will appear in validator output
148
+ or be apparent to any reader of the JSON.
149
+
150
+ - **Omitting sample size.** The field is required. There is no valid ARS benchmark report
151
+ without a stated `human_baseline.sample_size`. n=1 is worse than n=10, but it is
152
+ infinitely better than unstated.
153
+
154
+ - **Author-conducted with no caveat disclosure.** Using `author-conducted` is allowed.
155
+ Not noting it in `caveats` as a limitation is an editorial failure, not a schema
156
+ failure — but reviewers will notice.
157
+
158
+ - **Self-scoring with no warning acknowledgment.** `self-scored` produces a warning on
159
+ every validator run. If you publish a report with `self-scored` and don't address it
160
+ in caveats, the omission is visible in the JSON to anyone who checks.
161
+
162
+ - **Empty or single-word caveats.** The schema requires `minLength: 1` per item and
163
+ `minItems: 1` for the array. A caveat of `"none"` is technically valid but signals
164
+ that the author did not engage seriously with limitations.
165
+
166
+ - **Claiming ARS advantage without disclosing cost_usd.** The field is required. A claim
167
+ that "ARS completed this in 4 hours vs 40 human hours" without a dollar figure omits
168
+ the dimension where the trade-off may be reversed.
169
+
170
+ ---
171
+
172
+ ## Future evolution
173
+
174
+ Per-skill benchmark templates (a `deep-research`-specific template, an
175
+ `academic-paper-reviewer`-specific template) are likely as v3.4 adds domain-specific
176
+ evaluation protocols. The `cost_usd` field may split into `cost_usd_api` and
177
+ `cost_usd_compute` once cloud execution costs become a factor. The
178
+ `data_access_level_declared` enum may expand to match the v3.4 ground-truth tier
179
+ vocabulary if that spec evolves. None of these changes will break existing v3.3.5
180
+ reports, which remain valid against the version they declared in `ars_version`.