psyclaw 0.27.23 → 0.28.1

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 (1069) hide show
  1. package/README.md +11 -5
  2. package/agents/recommended/catalog.json +99 -0
  3. package/dist/apps/panel/index.html +5 -5
  4. package/dist/src/adapters/pi/extension.js +339 -94
  5. package/dist/src/adapters/pi/extension.js.map +1 -1
  6. package/dist/src/adapters/pi/rpc.d.ts +2 -0
  7. package/dist/src/adapters/pi/rpc.js +9 -2
  8. package/dist/src/adapters/pi/rpc.js.map +1 -1
  9. package/dist/src/agents/import.js +44 -32
  10. package/dist/src/agents/import.js.map +1 -1
  11. package/dist/src/agents/recommended-personas.d.ts +42 -0
  12. package/dist/src/agents/recommended-personas.js +135 -0
  13. package/dist/src/agents/recommended-personas.js.map +1 -0
  14. package/dist/src/analysis/hooks.d.ts +1 -0
  15. package/dist/src/analysis/hooks.js +20 -1
  16. package/dist/src/analysis/hooks.js.map +1 -1
  17. package/dist/src/ars/bridge.d.ts +20 -0
  18. package/dist/src/ars/bridge.js +132 -0
  19. package/dist/src/ars/bridge.js.map +1 -0
  20. package/dist/src/ars/contracts.d.ts +55 -0
  21. package/dist/src/ars/contracts.js +2 -0
  22. package/dist/src/ars/contracts.js.map +1 -0
  23. package/dist/src/ars/panel-plan.d.ts +4 -0
  24. package/dist/src/ars/panel-plan.js +11 -0
  25. package/dist/src/ars/panel-plan.js.map +1 -0
  26. package/dist/src/ars/pi-panel-executor.d.ts +30 -0
  27. package/dist/src/ars/pi-panel-executor.js +140 -0
  28. package/dist/src/ars/pi-panel-executor.js.map +1 -0
  29. package/dist/src/ars/profile.d.ts +36 -0
  30. package/dist/src/ars/profile.js +119 -0
  31. package/dist/src/ars/profile.js.map +1 -0
  32. package/dist/src/ars/re-review.d.ts +22 -0
  33. package/dist/src/ars/re-review.js +172 -0
  34. package/dist/src/ars/re-review.js.map +1 -0
  35. package/dist/src/branding.d.ts +2 -4
  36. package/dist/src/branding.js +3 -5
  37. package/dist/src/branding.js.map +1 -1
  38. package/dist/src/bundled-tools.d.ts +3 -0
  39. package/dist/src/bundled-tools.js +21 -0
  40. package/dist/src/bundled-tools.js.map +1 -0
  41. package/dist/src/chat.js +6 -5
  42. package/dist/src/chat.js.map +1 -1
  43. package/dist/src/cli.js +6 -3
  44. package/dist/src/cli.js.map +1 -1
  45. package/dist/src/creation/contracts.d.ts +41 -0
  46. package/dist/src/creation/contracts.js +2 -0
  47. package/dist/src/creation/contracts.js.map +1 -0
  48. package/dist/src/creation/service.d.ts +7 -0
  49. package/dist/src/creation/service.js +208 -0
  50. package/dist/src/creation/service.js.map +1 -0
  51. package/dist/src/index.d.ts +11 -0
  52. package/dist/src/index.js +11 -0
  53. package/dist/src/index.js.map +1 -1
  54. package/dist/src/install/installer.js +32 -10
  55. package/dist/src/install/installer.js.map +1 -1
  56. package/dist/src/orchestration/bundled-personas.d.ts +16 -0
  57. package/dist/src/orchestration/bundled-personas.js +101 -0
  58. package/dist/src/orchestration/bundled-personas.js.map +1 -0
  59. package/dist/src/orchestration/effects.d.ts +8 -0
  60. package/dist/src/orchestration/effects.js +39 -0
  61. package/dist/src/orchestration/effects.js.map +1 -0
  62. package/dist/src/orchestration/personas.d.ts +16 -0
  63. package/dist/src/orchestration/personas.js +64 -0
  64. package/dist/src/orchestration/personas.js.map +1 -0
  65. package/dist/src/orchestration/pi-executor.d.ts +9 -4
  66. package/dist/src/orchestration/pi-executor.js +55 -22
  67. package/dist/src/orchestration/pi-executor.js.map +1 -1
  68. package/dist/src/orchestration/research-agents.d.ts +3 -7
  69. package/dist/src/orchestration/research-agents.js +5 -69
  70. package/dist/src/orchestration/research-agents.js.map +1 -1
  71. package/dist/src/panel/server.js +19 -4
  72. package/dist/src/panel/server.js.map +1 -1
  73. package/dist/src/project/paths.d.ts +3 -0
  74. package/dist/src/project/paths.js +7 -0
  75. package/dist/src/project/paths.js.map +1 -1
  76. package/dist/src/rules/user-rules.d.ts +8 -0
  77. package/dist/src/rules/user-rules.js +36 -0
  78. package/dist/src/rules/user-rules.js.map +1 -0
  79. package/dist/src/skills/contracts.d.ts +4 -4
  80. package/dist/src/skills/recommended.js +1 -1
  81. package/dist/src/skills/registry.js +49 -28
  82. package/dist/src/skills/registry.js.map +1 -1
  83. package/dist/src/style/cli-ui.d.ts +14 -0
  84. package/dist/src/style/cli-ui.js +45 -1
  85. package/dist/src/style/cli-ui.js.map +1 -1
  86. package/dist/src/tui/skill-manager.js +1 -1
  87. package/dist/src/tui/skill-manager.js.map +1 -1
  88. package/dist/src/updates/update.js +9 -3
  89. package/dist/src/updates/update.js.map +1 -1
  90. package/package.json +15 -3
  91. package/scripts/rebrand-pi.mjs +6 -0
  92. package/skills/recommended/catalog.json +2 -11
  93. package/vendor/ars/.claude/CLAUDE.md +371 -0
  94. package/vendor/ars/.command-invariants.toml +24 -0
  95. package/vendor/ars/CITATION.cff +35 -0
  96. package/vendor/ars/LICENSE +417 -0
  97. package/vendor/ars/MODE_REGISTRY.md +76 -0
  98. package/vendor/ars/NOTICE.md +26 -0
  99. package/vendor/ars/POSITIONING.md +99 -0
  100. package/vendor/ars/PSYCLAW_SOURCE.json +10 -0
  101. package/vendor/ars/README.md +751 -0
  102. package/vendor/ars/SECURITY.md +52 -0
  103. package/vendor/ars/THIRD_PARTY.md +70 -0
  104. package/vendor/ars/academic-paper/SKILL.md +542 -0
  105. package/vendor/ars/academic-paper/agents/abstract_bilingual_agent.md +171 -0
  106. package/vendor/ars/academic-paper/agents/argument_builder_agent.md +276 -0
  107. package/vendor/ars/academic-paper/agents/citation_compliance_agent.md +422 -0
  108. package/vendor/ars/academic-paper/agents/draft_writer_agent.md +656 -0
  109. package/vendor/ars/academic-paper/agents/formatter_agent.md +999 -0
  110. package/vendor/ars/academic-paper/agents/intake_agent.md +393 -0
  111. package/vendor/ars/academic-paper/agents/literature_strategist_agent.md +626 -0
  112. package/vendor/ars/academic-paper/agents/peer_reviewer_agent.md +516 -0
  113. package/vendor/ars/academic-paper/agents/revision_coach_agent.md +334 -0
  114. package/vendor/ars/academic-paper/agents/socratic_mentor_agent.md +527 -0
  115. package/vendor/ars/academic-paper/agents/structure_architect_agent.md +401 -0
  116. package/vendor/ars/academic-paper/agents/visualization_agent.md +441 -0
  117. package/vendor/ars/academic-paper/examples/chinese_paper_example.md +278 -0
  118. package/vendor/ars/academic-paper/examples/clinical_citation_verification_checklist.md +95 -0
  119. package/vendor/ars/academic-paper/examples/clinical_epistemic_status_example.md +100 -0
  120. package/vendor/ars/academic-paper/examples/commitment_ledger_example.md +147 -0
  121. package/vendor/ars/academic-paper/examples/imrad_hei_example.md +234 -0
  122. package/vendor/ars/academic-paper/examples/literature_review_example.md +260 -0
  123. package/vendor/ars/academic-paper/examples/plan_mode_guided_writing.md +600 -0
  124. package/vendor/ars/academic-paper/examples/revision_mode_example.md +344 -0
  125. package/vendor/ars/academic-paper/examples/revision_recovery_example.md +506 -0
  126. package/vendor/ars/academic-paper/examples/version_family_reconciliation_example.md +89 -0
  127. package/vendor/ars/academic-paper/references/abstract_writing_guide.md +169 -0
  128. package/vendor/ars/academic-paper/references/academic_writing_style.md +188 -0
  129. package/vendor/ars/academic-paper/references/anti_leakage_protocol.md +83 -0
  130. package/vendor/ars/academic-paper/references/apa7_chinese_citation_guide.md +364 -0
  131. package/vendor/ars/academic-paper/references/apa7_extended_guide.md +198 -0
  132. package/vendor/ars/academic-paper/references/changelog.md +11 -0
  133. package/vendor/ars/academic-paper/references/citation_format_switcher.md +228 -0
  134. package/vendor/ars/academic-paper/references/committee_correspondence_protocol.md +158 -0
  135. package/vendor/ars/academic-paper/references/credit_authorship_guide.md +308 -0
  136. package/vendor/ars/academic-paper/references/disclosure_mode_protocol.md +478 -0
  137. package/vendor/ars/academic-paper/references/domain_evidence_profiles.md +38 -0
  138. package/vendor/ars/academic-paper/references/failure_paths.md +349 -0
  139. package/vendor/ars/academic-paper/references/funding_statement_guide.md +319 -0
  140. package/vendor/ars/academic-paper/references/hei_domain_glossary.md +169 -0
  141. package/vendor/ars/academic-paper/references/intro_title_rhetoric_guide.md +114 -0
  142. package/vendor/ars/academic-paper/references/journal_submission_guide.md +249 -0
  143. package/vendor/ars/academic-paper/references/latex_template_reference.md +378 -0
  144. package/vendor/ars/academic-paper/references/mode_selection_guide.md +378 -0
  145. package/vendor/ars/academic-paper/references/paper_structure_patterns.md +330 -0
  146. package/vendor/ars/academic-paper/references/plan_mode_protocol.md +112 -0
  147. package/vendor/ars/academic-paper/references/policy_anchor_disclosure_protocol.md +200 -0
  148. package/vendor/ars/academic-paper/references/policy_anchor_table.md +157 -0
  149. package/vendor/ars/academic-paper/references/revision_patch_protocol.md +173 -0
  150. package/vendor/ars/academic-paper/references/statistical_visualization_standards.md +750 -0
  151. package/vendor/ars/academic-paper/references/venue_disclosure_policies.md +259 -0
  152. package/vendor/ars/academic-paper/references/vlm_figure_verification.md +126 -0
  153. package/vendor/ars/academic-paper/references/workflow_phase_details.md +135 -0
  154. package/vendor/ars/academic-paper/references/writing_judgment_framework.md +59 -0
  155. package/vendor/ars/academic-paper/references/writing_quality_check.md +173 -0
  156. package/vendor/ars/academic-paper/templates/bilingual_abstract_template.md +78 -0
  157. package/vendor/ars/academic-paper/templates/case_study_template.md +129 -0
  158. package/vendor/ars/academic-paper/templates/conference_paper_template.md +108 -0
  159. package/vendor/ars/academic-paper/templates/credit_statement_template.md +132 -0
  160. package/vendor/ars/academic-paper/templates/funding_statement_template.md +290 -0
  161. package/vendor/ars/academic-paper/templates/imrad_template.md +183 -0
  162. package/vendor/ars/academic-paper/templates/latex_article_template.tex +199 -0
  163. package/vendor/ars/academic-paper/templates/literature_review_template.md +135 -0
  164. package/vendor/ars/academic-paper/templates/policy_brief_template.md +139 -0
  165. package/vendor/ars/academic-paper/templates/revision_tracking_template.md +199 -0
  166. package/vendor/ars/academic-paper/templates/theoretical_paper_template.md +119 -0
  167. package/vendor/ars/academic-paper-reviewer/SKILL.md +491 -0
  168. package/vendor/ars/academic-paper-reviewer/agents/devils_advocate_reviewer_agent.md +443 -0
  169. package/vendor/ars/academic-paper-reviewer/agents/domain_reviewer_agent.md +412 -0
  170. package/vendor/ars/academic-paper-reviewer/agents/editorial_synthesizer_agent.md +478 -0
  171. package/vendor/ars/academic-paper-reviewer/agents/eic_agent.md +339 -0
  172. package/vendor/ars/academic-paper-reviewer/agents/field_analyst_agent.md +221 -0
  173. package/vendor/ars/academic-paper-reviewer/agents/methodology_reviewer_agent.md +449 -0
  174. package/vendor/ars/academic-paper-reviewer/agents/perspective_reviewer_agent.md +427 -0
  175. package/vendor/ars/academic-paper-reviewer/examples/hei_paper_review_example.md +391 -0
  176. package/vendor/ars/academic-paper-reviewer/examples/interdisciplinary_review_example.md +299 -0
  177. package/vendor/ars/academic-paper-reviewer/examples/subclaim_decomposition_example.md +80 -0
  178. package/vendor/ars/academic-paper-reviewer/references/calibration_mode_protocol.md +256 -0
  179. package/vendor/ars/academic-paper-reviewer/references/changelog.md +10 -0
  180. package/vendor/ars/academic-paper-reviewer/references/editorial_decision_standards.md +236 -0
  181. package/vendor/ars/academic-paper-reviewer/references/guided_mode_protocol.md +34 -0
  182. package/vendor/ars/academic-paper-reviewer/references/integration_guide.md +15 -0
  183. package/vendor/ars/academic-paper-reviewer/references/quality_rubrics.md +84 -0
  184. package/vendor/ars/academic-paper-reviewer/references/re_review_mode_protocol.md +340 -0
  185. package/vendor/ars/academic-paper-reviewer/references/review_criteria_framework.md +98 -0
  186. package/vendor/ars/academic-paper-reviewer/references/review_panel_provenance_protocol.md +197 -0
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  188. package/vendor/ars/academic-paper-reviewer/references/reviewer_sprint_prompt_source.md +324 -0
  189. package/vendor/ars/academic-paper-reviewer/references/sprint_contract_protocol.md +296 -0
  190. package/vendor/ars/academic-paper-reviewer/references/statistical_reporting_standards.md +505 -0
  191. package/vendor/ars/academic-paper-reviewer/references/top_journals_by_field.md +206 -0
  192. package/vendor/ars/academic-paper-reviewer/templates/editorial_decision_template.md +235 -0
  193. package/vendor/ars/academic-paper-reviewer/templates/peer_review_report_template.md +305 -0
  194. package/vendor/ars/academic-paper-reviewer/templates/revision_response_template.md +248 -0
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  196. package/vendor/ars/academic-pipeline/agents/claim_ref_alignment_audit_agent.md +382 -0
  197. package/vendor/ars/academic-pipeline/agents/collaboration_depth_agent.md +164 -0
  198. package/vendor/ars/academic-pipeline/agents/integrity_verification_agent.md +870 -0
  199. package/vendor/ars/academic-pipeline/agents/pipeline_orchestrator_agent.md +1379 -0
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  204. package/vendor/ars/academic-pipeline/references/adapters/.gitkeep +0 -0
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  225. package/vendor/ars/agents/report_compiler_agent.md +341 -0
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  229. package/vendor/ars/commands/ars-abstract.md +10 -0
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@@ -0,0 +1,378 @@
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+ # Mode Selection Guide
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+
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+ This guide helps users and the `intake_agent` select the most appropriate operational mode.
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+
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+ ---
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+
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+ ## Mode Selection Flowchart
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+
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+ ```
10
+ User Input →
11
+ │
12
+ ├── Already have complete research?
13
+ │ ├── Yes → Want a full paper?
14
+ │ │ ├── Yes ─────────────────────────→ full mode
15
+ │ │ └── No → Just need an outline?
16
+ │ │ ├── Yes ─────────────────────→ outline-only mode
17
+ │ │ └── No → Just need an abstract?
18
+ │ │ ├── Yes ──────────────────→ abstract-only mode
19
+ │ │ └── No → Just need a literature review?
20
+ │ │ ├── Yes ─────────────→ lit-review mode
21
+ │ │ └── No ──────────────→ full mode
22
+ │ │
23
+ │ └── No → Want guided thinking?
24
+ │ ├── Yes ─────────────────────────→ plan mode ★ NEW
25
+ │ └── No ──────────────────────────→ full mode (Phase 0 will conduct an interview)
26
+ │
27
+ ├── Have an existing paper to revise? ──────────────────────→ revision mode
28
+ ├── Have comments explicitly identified as coming from a real committee or institutional review office?
29
+ │ └── Need tracking / response preparation ───────────────→ revision-coach committee-correspondence variant
30
+ ├── Have reviewer comments to handle?
31
+ │ ├── Comments only, no response written yet ──────────→ revision-coach mode
32
+ │ └── Comments + an existing rebuttal/response draft ──→ rebuttal-audit mode
33
+ ├── Need an AI-usage disclosure statement? ─────────────────→ disclosure mode
34
+ ├── Just need format conversion? ────────────────────────→ format-convert mode
35
+ └── Just need a citation check? ────────────────────────→ citation-check mode
36
+ ```
37
+
38
+ ---
39
+
40
+ ## Detailed Description of Each Mode
41
+
42
+ ### full mode — Complete Paper Writing
43
+
44
+ **Applicable Scenarios**:
45
+ - User has a clear research question and (partial) materials
46
+ - Needs to produce a complete paper from start to finish
47
+ - Includes all phases: Interview → Literature → Structure → Argumentation → Writing → Citation → Review → Formatting
48
+
49
+ **Not Applicable When**:
50
+ - User has no idea about research direction (→ use `deep-research` first)
51
+ - Only need a specific section (→ use another specialized mode)
52
+
53
+ **Expected Output**: Complete paper draft + references + bilingual abstract + review report
54
+ **Expected Duration**: Long (all 8 Phases fully executed)
55
+ **Agents Used**: All 9 + socratic_mentor (if needed)
56
+
57
+ ---
58
+
59
+ ### outline-only mode — Outline Generation
60
+
61
+ **Applicable Scenarios**:
62
+ - Only need the paper structure and outline
63
+ - A proposal to submit to an advisor for review
64
+ - Need to quickly plan the paper structure
65
+
66
+ **Not Applicable When**:
67
+ - Need complete paper content (→ full mode)
68
+ - Need guided thinking (→ plan mode)
69
+
70
+ **Expected Output**: Detailed outline + evidence allocation + word count distribution
71
+ **Expected Duration**: Short (Phase 0-2)
72
+ **Agents Used**: intake → literature_strategist → structure_architect
73
+
74
+ ---
75
+
76
+ ### plan mode — Chapter-by-Chapter Guided Planning ★ NEW
77
+
78
+ **Applicable Scenarios**:
79
+ - User has ideas but they are not yet clear enough
80
+ - Wants guided thinking for each chapter's content
81
+ - First-time academic paper writer
82
+ - Wants to think through every section before writing
83
+ - Just received materials from deep-research and needs to transform them into a paper plan
84
+
85
+ **Not Applicable When**:
86
+ - Already knows exactly what to write (→ full mode is faster)
87
+ - Only needs an outline without deep thinking (→ outline-only mode)
88
+ - Time-pressured and needs rapid output (→ full mode)
89
+
90
+ **Expected Output**: Chapter Plan + INSIGHT Collection
91
+ **Expected Duration**: Medium (Step 0-3, approximately 20-30 rounds of conversation)
92
+ **Agents Used**: intake → socratic_mentor → structure_architect → argument_builder
93
+
94
+ **Subsequent Connections**:
95
+ - Chapter Plan → full mode (produce complete paper)
96
+ - Chapter Plan → academic-paper-reviewer (review the plan)
97
+
98
+ ---
99
+
100
+ ### revision mode — Paper Revision
101
+
102
+ **Applicable Scenarios**:
103
+ - Already have a completed paper draft
104
+ - Received reviewer comments requiring revision
105
+ - Feel certain sections need improvement
106
+
107
+ **Not Applicable When**:
108
+ - No existing paper draft (→ full mode)
109
+ - Only need to check citation format (→ citation-check mode)
110
+
111
+ **Expected Output**: Revised paper + revision notes (tracked changes)
112
+ **Expected Duration**: Medium
113
+ **Agents Used**: peer_reviewer → draft_writer → citation_compliance
114
+
115
+ **Prerequisite**: User must provide existing paper content
116
+
117
+ ---
118
+
119
+ ### abstract-only mode — Abstract Writing
120
+
121
+ **Applicable Scenarios**:
122
+ - Paper is already complete, only need an abstract
123
+ - Need to submit a conference abstract
124
+ - Need a bilingual abstract
125
+
126
+ **Not Applicable When**:
127
+ - No paper content to summarize (→ full mode or plan mode)
128
+
129
+ **Expected Output**: Bilingual abstract (zh-TW + EN) + keywords
130
+ **Expected Duration**: Short
131
+ **Agents Used**: intake → abstract_bilingual
132
+
133
+ ---
134
+
135
+ ### lit-review mode — Literature Review
136
+
137
+ **Applicable Scenarios**:
138
+ - Need a literature review on a specific topic
139
+ - Preparing the Literature Review chapter of a paper
140
+ - Need a systematic search strategy and literature matrix
141
+
142
+ **Not Applicable When**:
143
+ - Need a complete paper (→ full mode)
144
+ - Need an in-depth research investigation (→ deep-research)
145
+
146
+ **Expected Output**: Annotated bibliography + literature matrix + synthesis analysis
147
+ **Expected Duration**: Medium
148
+ **Agents Used**: intake → literature_strategist
149
+
150
+ ---
151
+
152
+ ### format-convert mode — Format Conversion
153
+
154
+ **Applicable Scenarios**:
155
+ - Already have paper content, need format conversion
156
+ - Markdown → LaTeX / DOCX / PDF
157
+ - Need to comply with a specific journal's formatting requirements
158
+
159
+ **Not Applicable When**:
160
+ - No existing content (→ full mode)
161
+ - Need content modifications (→ revision mode)
162
+
163
+ **Expected Output**: Document in target format
164
+ **Expected Duration**: Short
165
+ **Agents Used**: formatter used standalone
166
+
167
+ ---
168
+
169
+ ### citation-check mode — Citation Check
170
+
171
+ **Applicable Scenarios**:
172
+ - Already have a paper, only need to check citation format
173
+ - Final check before submission
174
+ - Switching citation format (e.g., APA → IEEE)
175
+
176
+ **Not Applicable When**:
177
+ - No existing citation list (→ full mode)
178
+ - Need to modify paper content (→ revision mode)
179
+
180
+ **Expected Output**: Citation error report + automatic correction suggestions
181
+ **Expected Duration**: Short
182
+ **Agents Used**: citation_compliance used standalone
183
+
184
+ ---
185
+
186
+ ### revision-coach mode — Reviewer-Comment Triage
187
+
188
+ **Applicable Scenarios**:
189
+ - Received reviewer comments / a decision letter and need them parsed into a structured plan
190
+ - Want a Revision Roadmap that classifies, maps, and prioritizes each comment
191
+ - Need a Response Letter Skeleton to start drafting replies
192
+ - Deciding whether to address or push back on a comment (disagreement posture)
193
+ - Non-journal scopes: conference rebuttal, grant-panel response, transfer-after-review
194
+
195
+ **Not Applicable When**:
196
+ - Already have a written rebuttal/response draft you want QA'd (→ rebuttal-audit mode)
197
+ - The paper itself needs rewriting based on the comments (→ revision mode)
198
+
199
+ **Expected Output**: Revision Roadmap + optional Tracking Template + Response Letter Skeleton
200
+ **Expected Duration**: Short-Medium
201
+ **Agents Used**: revision_coach_agent used standalone (no prior pipeline execution required)
202
+
203
+ **Committee-correspondence variant**: when the user explicitly identifies comments
204
+ from a real committee or institutional review office, this same entrypoint loads
205
+ `committee_correspondence_protocol.md` and emits the separate #668 byte-accounted
206
+ concern tracker plus placeholder response skeleton. It does not emit the reviewer
207
+ Roadmap, Schema 11, priority/severity, a determination, or a resolution claim. Formal
208
+ tone alone never activates the variant.
209
+
210
+ ---
211
+
212
+ ### disclosure mode — AI-Usage Disclosure Outcome
213
+
214
+ **Applicable Scenarios**:
215
+ - Paper is drafted and you need venue-specific disclosure text or a policy action checklist
216
+ - Submitting under a covered policy target (ICLR, NeurIPS, Nature, Science, ACL, EMNLP, or a covered medical-publishing target: ICMJE, NEJM, The Lancet, JAMA, BMJ, PLOS, Frontiers, publisher-wide 中华护理杂志社, journal-level 国际眼科杂志)
217
+ - Need placement/action guidance for every required manuscript or submission channel
218
+
219
+ **Not Applicable When**:
220
+ - No paper drafted yet — disclosure is a finishing step (→ full mode first)
221
+ - The venue is not in the policy database (confirm the venue's current policy manually)
222
+
223
+ **Expected Output**: Default venue path — `REQUIRED` / `ACTION_ONLY` / `NOT_REQUIRED` / `UNKNOWN` applicability plus typed halt status; policy-anchor path — anchor-specific render
224
+ **Expected Duration**: Short
225
+ **Agents Used**: formatter agent's standalone disclosure branch, which loads the disclosure protocol before the venue policy database or policy-anchor lookup; it does not run normal Phase 7 formatting
226
+
227
+ ---
228
+
229
+ ### rebuttal-audit mode — Rebuttal-Draft QA
230
+
231
+ **Applicable Scenarios**:
232
+ - You already wrote a rebuttal/response-to-reviewers draft and want it checked before sending
233
+ - Need a per-comment coverage table (which reviewer concerns the draft addresses, partially addresses, or misses)
234
+ - Want risk flags for tone (too combative), unsupported claims, or a response that misreads the reviewer's point
235
+
236
+ **Not Applicable When**:
237
+ - You have reviewer comments but have **not** written a response yet (→ revision-coach mode, which *generates* a skeleton)
238
+ - The manuscript itself needs revising (→ revision mode)
239
+
240
+ **Input gate**: requires BOTH (a) the reviewer comments / decision letter AND (b) an existing rebuttal draft. Comments only → route to revision-coach. If intent is ambiguous, clarify rather than guess.
241
+
242
+ **Expected Output**: Advisory QA report — per-comment coverage + gap list + risk flags. Generates no new response.
243
+ **Expected Duration**: Short
244
+ **Agents Used**: revision_coach_agent's comment-parsing capability, run standalone (advisory)
245
+
246
+ **Integrity boundary**: a standalone invocation runs **outside** the pipeline, so rebuttal-audit does **not** emit a Schema 11 ledger, does **not** write the Material Passport, and does **not** mark anything `ready_to_submit` or verified. The output is advisory QA only.
247
+
248
+ ---
249
+
250
+ ## Paths from deep-research
251
+
252
+ ```
253
+ deep-research completed
254
+ │
255
+ ├── deep-research (full mode) outputs:
256
+ │ RQ Brief + Methodology Blueprint + Annotated Bibliography + Synthesis Report
257
+ │ │
258
+ │ ├── Want to write the paper directly ──→ academic-paper (full mode)
259
+ │ │ intake_agent auto-detects materials, skips redundant questions
260
+ │ │
261
+ │ └── Want to plan before writing ──→ academic-paper (plan mode)
262
+ │ socratic_mentor leverages existing materials to accelerate guidance
263
+ │
264
+ └── deep-research (socratic mode) outputs:
265
+ INSIGHT Collection + Synthesis Report
266
+ │
267
+ ├── INSIGHTs are sufficiently clear ──→ academic-paper (full mode)
268
+ │
269
+ └── Need more guidance ──→ academic-paper (plan mode)
270
+ socratic_mentor continues deepening from INSIGHTs
271
+ ```
272
+
273
+ ## Connecting to academic-paper-reviewer
274
+
275
+ ```
276
+ academic-paper completed
277
+ │
278
+ ├── full mode produces complete paper ──→ academic-paper-reviewer (full / guided)
279
+ │ Complete peer review + revision suggestions
280
+ │
281
+ ├── plan mode produces Chapter Plan ──→ academic-paper-reviewer (guided)
282
+ │ Review the plan's feasibility and completeness
283
+ │
284
+ └── reviewer feedback ──→ academic-paper (revision mode)
285
+ Revise paper based on review comments
286
+ ```
287
+
288
+ ---
289
+
290
+ ## Common Misselection Scenarios
291
+
292
+ | User Says | Easily Misselected | Correct Choice | Reason |
293
+ |---------|---------|---------|------|
294
+ | "Help me write an outline" / 「幫我寫大綱」 | outline-only | First confirm: Do they want a simple outline or deep planning? | May need plan mode |
295
+ | "I want to write a paper but don't know how to start" / 「想寫論文但不知道怎麼開始」 | full | plan mode | Needs guided thinking |
296
+ | "Help me revise my paper" / 「幫我修改論文」 | revision | First confirm: Are there reviewer comments? | May need full mode rewrite |
297
+ | "Help me search for literature" / 「幫我找文獻」 | lit-review | First confirm: Is it a literature review for a paper or a research investigation? | May need deep-research |
298
+ | "I have deep-research results, help me write a paper" / 「我有研究結果,幫我寫成論文」 | full (skip Phase 0 directly) | full (but intake needs to detect handoff) | Materials need to be properly imported |
299
+ | "I want to plan my paper step by step" / 「我想逐步規劃論文」 | outline-only | plan mode | Needs interactive guidance |
300
+ | "The paper format is wrong" / 「論文格式不對」 | revision | citation-check or format-convert | May only need format correction |
301
+ | 「帶我寫論文」/「引導我寫論文」 | full | plan mode | 使用者需要互動式引導,不是直接產出 |
302
+ | 「第一次寫論文」/「論文新手」 | full | plan mode | 新手需要蘇格拉底式逐章引導 |
303
+
304
+ ---
305
+
306
+ ## Quick Decision Table
307
+
308
+ | What Do You Have? | What Do You Want? | Choose This Mode |
309
+ |-----------|-----------|------------|
310
+ | Nothing | Complete paper | plan mode → full mode |
311
+ | Research question + literature | Complete paper | full mode |
312
+ | Research question + literature | Outline | outline-only mode |
313
+ | Vague idea | Paper plan | plan mode |
314
+ | deep-research results | Complete paper | full mode (auto-handoff) |
315
+ | deep-research results | Guided planning | plan mode |
316
+ | Completed paper | Revision | revision mode |
317
+ | Completed paper | Abstract | abstract-only mode |
318
+ | Completed paper | Format conversion | format-convert mode |
319
+ | Completed paper | Citation check | citation-check mode |
320
+ | Reviewer comments (no response yet) | Parse + roadmap + reply skeleton | revision-coach mode |
321
+ | Real-committee comments (explicitly identified; no response yet) | Preserve source + concern tracker + placeholder response skeleton | revision-coach committee-correspondence variant |
322
+ | Reviewer comments + a written rebuttal draft | QA the draft before sending | rebuttal-audit mode |
323
+ | Drafted paper + target venue | AI-usage disclosure bundle or policy action checklist | disclosure mode |
324
+
325
+ ---
326
+
327
+ ### Plan to Full Mode Conversion Protocol
328
+
329
+ When a user completes `plan` mode and wants to proceed to `full` mode for actual paper writing:
330
+
331
+ #### Conversion Checklist
332
+
333
+ | Plan Mode Output | Full Mode Input | Conversion Action |
334
+ |-----------------|-----------------|-------------------|
335
+ | Chapter Plan (structure outline) | `structure_architect` agent | Map chapters → formal sections with heading levels; validate against `paper_structure_patterns.md` |
336
+ | Socratic Responses (Q&A transcripts) | `argument_builder` agent | Extract claims + evidence + warrants from dialogue; discard conversational scaffolding |
337
+ | Literature Notes (if any) | `literature_strategist` agent | Independent execution — plan mode notes serve as seed keywords only; full systematic search required |
338
+ | Argument Sketches | `argument_builder` agent | Evaluate each sketch against 4-level scoring; only `adequate` or above proceed |
339
+
340
+ #### Quality Gate
341
+
342
+ Before conversion, ALL of the following must be true:
343
+ - [ ] Every chapter in the Chapter Plan has at least 1 argument sketch rated `adequate` or above
344
+ - [ ] The overall paper structure maps to a recognized pattern in `paper_structure_patterns.md`
345
+ - [ ] At least 5 potential references have been identified (seeds for `literature_strategist`)
346
+ - [ ] The research question is finalized (not still evolving from Socratic dialogue)
347
+
348
+ #### What Gets Discarded
349
+ - Conversational filler from Socratic dialogue (greetings, confirmations, repetitions)
350
+ - Tentative ideas explicitly marked as "maybe" or "not sure" by the user
351
+ - Plan mode's iterative drafts (only the final version of each chapter plan carries over)
352
+
353
+ ---
354
+
355
+ ## Trigger-to-Mode Mapping Examples
356
+
357
+ ```
358
+ "Write a paper on SDGs in HEI" -> full
359
+ "Give me a paper outline for..." -> outline-only
360
+ "Revise this paper based on feedback" -> revision
361
+ "Write an abstract for this paper" -> abstract-only
362
+ "Do a literature review on..." -> lit-review
363
+ "Convert this paper to LaTeX" -> format-convert
364
+ "Convert citations to IEEE" -> format-convert
365
+ "Check the citations in this paper" -> citation-check
366
+ "guide my paper" -> plan
367
+ "help me plan my paper" -> plan
368
+ "I got reviewer comments" -> revision-coach
369
+ "parse these reviews" -> revision-coach
370
+ "help me with my revision" -> revision-coach
371
+ "should we push back on reviewer 2" -> revision-coach
372
+ "conference rebuttal" / "grant response" -> revision-coach
373
+ "track these committee comments" -> revision-coach committee-correspondence variant (only with explicit real-source identity)
374
+ "audit my rebuttal draft" -> rebuttal-audit (needs comments + an existing draft)
375
+ "did I miss any reviewer comment" -> rebuttal-audit
376
+ "AI disclosure for Nature" -> disclosure
377
+ "generate an AI usage statement" -> disclosure
378
+ ```
@@ -0,0 +1,330 @@
1
+ # Paper Structure Patterns — 6 Paper Structure Models
2
+
3
+ Used by `structure_architect_agent` and `intake_agent` to select the appropriate paper structure.
4
+
5
+ ## Pattern 1: IMRaD (Introduction-Method-Results-Discussion)
6
+
7
+ **Best for**: Empirical research with original data collection and analysis
8
+ **Typical length**: 5,000-8,000 words
9
+ **Disciplines**: Sciences, Social Sciences, Education, Medicine
10
+
11
+ ### Structure
12
+
13
+ ```
14
+ 1. Title Page
15
+ 2. Abstract (150-250 words)
16
+ Keywords (5-7)
17
+ 3. Introduction
18
+ 3.1 Context and Background
19
+ 3.2 Problem Statement
20
+ 3.3 Research Gap
21
+ 3.4 Purpose and Research Questions
22
+ 3.5 Significance of the Study
23
+ 4. Literature Review
24
+ 4.1 Theoretical Framework
25
+ 4.2 Theme 1: [related research]
26
+ 4.3 Theme 2: [related research]
27
+ 4.4 Theme 3: [related research]
28
+ 4.5 Summary and Conceptual Framework
29
+ 5. Methodology
30
+ 5.1 Research Design
31
+ 5.2 Participants/Sample
32
+ 5.3 Data Collection
33
+ 5.4 Instruments/Measures
34
+ 5.5 Data Analysis
35
+ 5.6 Validity and Reliability
36
+ 5.7 Ethical Considerations
37
+ 6. Results/Findings
38
+ 6.1 Descriptive Statistics (if quantitative)
39
+ 6.2 Finding 1 (aligned with RQ1)
40
+ 6.3 Finding 2 (aligned with RQ2)
41
+ 6.4 Finding 3 (if applicable)
42
+ 7. Discussion
43
+ 7.1 Summary of Findings
44
+ 7.2 Interpretation and Comparison with Literature
45
+ 7.3 Theoretical Implications
46
+ 7.4 Practical Implications
47
+ 7.5 Limitations
48
+ 7.6 Future Research Directions
49
+ 8. Conclusion
50
+ 9. References
51
+ 10. Appendices (if applicable)
52
+ ```
53
+
54
+ ### Word Allocation (6,000-word example)
55
+ | Section | % | Words |
56
+ |---------|---|-------|
57
+ | Introduction | 15% | 900 |
58
+ | Literature Review | 25% | 1,500 |
59
+ | Methodology | 15% | 900 |
60
+ | Results | 20% | 1,200 |
61
+ | Discussion | 20% | 1,200 |
62
+ | Conclusion | 5% | 300 |
63
+
64
+ ---
65
+
66
+ ## Pattern 2: Thematic Literature Review
67
+
68
+ **Best for**: Synthesizing existing research, identifying gaps, proposing future directions
69
+ **Typical length**: 6,000-10,000 words
70
+ **Disciplines**: All (especially Social Sciences, Education, Humanities)
71
+
72
+ ### Structure
73
+
74
+ ```
75
+ 1. Title Page
76
+ 2. Abstract
77
+ Keywords
78
+ 3. Introduction
79
+ 3.1 Topic and Rationale
80
+ 3.2 Scope and Boundaries
81
+ 3.3 Review Methodology (search strategy, inclusion criteria)
82
+ 3.4 Organization of the Review
83
+ 4. Theme 1: [descriptive title]
84
+ 4.1 Sub-theme A
85
+ 4.2 Sub-theme B
86
+ 4.3 Summary of Theme 1
87
+ 5. Theme 2: [descriptive title]
88
+ 5.1 Sub-theme A
89
+ 5.2 Sub-theme B
90
+ 5.3 Summary of Theme 2
91
+ 6. Theme 3: [descriptive title]
92
+ 6.1 Sub-theme A
93
+ 6.2 Sub-theme B
94
+ 6.3 Summary of Theme 3
95
+ 7. Cross-Cutting Synthesis
96
+ 7.1 Convergent Findings
97
+ 7.2 Divergent Findings and Debates
98
+ 7.3 Methodological Observations
99
+ 8. Research Gaps and Future Directions
100
+ 8.1 Identified Gaps
101
+ 8.2 Proposed Research Agenda
102
+ 9. Conclusion
103
+ 9.1 Key Takeaways
104
+ 9.2 Implications for Practice/Policy
105
+ 10. References
106
+ ```
107
+
108
+ ### Word Allocation (8,000-word example)
109
+ | Section | % | Words |
110
+ |---------|---|-------|
111
+ | Introduction | 10% | 800 |
112
+ | Theme 1 | 20% | 1,600 |
113
+ | Theme 2 | 20% | 1,600 |
114
+ | Theme 3 | 20% | 1,600 |
115
+ | Synthesis | 15% | 1,200 |
116
+ | Gaps & Future | 10% | 800 |
117
+ | Conclusion | 5% | 400 |
118
+
119
+ ---
120
+
121
+ ## Pattern 3: Theoretical Analysis
122
+
123
+ **Best for**: Developing, critiquing, or extending theoretical frameworks
124
+ **Typical length**: 5,000-8,000 words
125
+ **Disciplines**: Social Sciences, Philosophy, Education
126
+
127
+ ### Structure
128
+
129
+ ```
130
+ 1. Title Page
131
+ 2. Abstract
132
+ Keywords
133
+ 3. Introduction
134
+ 3.1 The Theoretical Problem
135
+ 3.2 Why This Theory Matters
136
+ 3.3 Purpose and Contribution
137
+ 4. Background: The Theory in Context
138
+ 4.1 Origins and Development
139
+ 4.2 Key Concepts and Definitions
140
+ 4.3 Current State of the Theory
141
+ 5. Critical Analysis
142
+ 5.1 Strengths of the Framework
143
+ 5.2 Limitations and Gaps
144
+ 5.3 Competing Perspectives
145
+ 5.4 Empirical Support (or lack thereof)
146
+ 6. Proposed Extension/Revision
147
+ 6.1 New Dimensions or Modifications
148
+ 6.2 Conceptual Model
149
+ 6.3 Propositions for Testing
150
+ 7. Applications and Implications
151
+ 7.1 Theoretical Implications
152
+ 7.2 Practical Applications
153
+ 7.3 Methodological Implications
154
+ 8. Conclusion
155
+ 8.1 Summary of Contribution
156
+ 8.2 Limitations of the Analysis
157
+ 8.3 Future Directions
158
+ 9. References
159
+ ```
160
+
161
+ ### Word Allocation (6,000-word example)
162
+ | Section | % | Words |
163
+ |---------|---|-------|
164
+ | Introduction | 12% | 720 |
165
+ | Background | 20% | 1,200 |
166
+ | Critical Analysis | 28% | 1,680 |
167
+ | Extension | 20% | 1,200 |
168
+ | Applications | 15% | 900 |
169
+ | Conclusion | 5% | 300 |
170
+
171
+ ---
172
+
173
+ ## Pattern 4: Case Study
174
+
175
+ **Best for**: In-depth analysis of specific institutions, programs, events, or phenomena
176
+ **Typical length**: 4,000-7,000 words
177
+ **Disciplines**: Education, Business, Social Sciences, Medicine (clinical)
178
+
179
+ ### Structure
180
+
181
+ ```
182
+ 1. Title Page
183
+ 2. Abstract
184
+ Keywords
185
+ 3. Introduction
186
+ 3.1 Background and Rationale
187
+ 3.2 Case Selection Justification
188
+ 3.3 Research Questions
189
+ 4. Literature Context
190
+ 4.1 Relevant Theoretical Framework
191
+ 4.2 Prior Research on Similar Cases
192
+ 5. Case Description
193
+ 5.1 Context and Setting
194
+ 5.2 Key Actors and Stakeholders
195
+ 5.3 Timeline of Events
196
+ 5.4 Data Sources
197
+ 6. Analysis
198
+ 6.1 Analysis Framework
199
+ 6.2 Theme/Finding 1
200
+ 6.3 Theme/Finding 2
201
+ 6.4 Theme/Finding 3
202
+ 7. Discussion
203
+ 7.1 Cross-Theme Synthesis
204
+ 7.2 Comparison with Literature
205
+ 7.3 Theoretical Insights
206
+ 7.4 Transferability (not generalizability)
207
+ 8. Lessons Learned and Recommendations
208
+ 8.1 For Practitioners
209
+ 8.2 For Policymakers
210
+ 8.3 For Researchers
211
+ 9. Conclusion
212
+ 10. References
213
+ 11. Appendices (case documents, data)
214
+ ```
215
+
216
+ ### Word Allocation (5,000-word example)
217
+ | Section | % | Words |
218
+ |---------|---|-------|
219
+ | Introduction | 12% | 600 |
220
+ | Literature | 15% | 750 |
221
+ | Case Description | 20% | 1,000 |
222
+ | Analysis | 25% | 1,250 |
223
+ | Discussion | 18% | 900 |
224
+ | Recommendations | 7% | 350 |
225
+ | Conclusion | 3% | 150 |
226
+
227
+ ---
228
+
229
+ ## Pattern 5: Policy Brief
230
+
231
+ **Best for**: Evidence-based policy recommendations for decision-makers
232
+ **Typical length**: 2,000-4,000 words
233
+ **Disciplines**: Public Policy, Education, Health, Economics
234
+
235
+ ### Structure
236
+
237
+ ```
238
+ 1. Title and Author Information
239
+ 2. Executive Summary (200-300 words)
240
+ Key recommendations (3-5 bullet points)
241
+ 3. Background
242
+ 3.1 The Policy Problem
243
+ 3.2 Current Policy Context
244
+ 3.3 Why Action is Needed Now
245
+ 4. Evidence Base
246
+ 4.1 Key Finding 1
247
+ 4.2 Key Finding 2
248
+ 4.3 Key Finding 3
249
+ 4.4 International Comparisons (if relevant)
250
+ 5. Policy Options Analysis
251
+ 5.1 Option A: [description]
252
+ - Pros / Cons / Cost / Feasibility
253
+ 5.2 Option B: [description]
254
+ - Pros / Cons / Cost / Feasibility
255
+ 5.3 Option C: [description]
256
+ - Pros / Cons / Cost / Feasibility
257
+ 6. Recommendations
258
+ 6.1 Recommended Option with Justification
259
+ 6.2 Implementation Steps
260
+ 6.3 Timeline
261
+ 6.4 Success Metrics
262
+ 7. Conclusion
263
+ 8. References
264
+ 9. Appendix: Methodology Note
265
+ ```
266
+
267
+ ### Word Allocation (3,000-word example)
268
+ | Section | % | Words |
269
+ |---------|---|-------|
270
+ | Executive Summary | 10% | 300 |
271
+ | Background | 15% | 450 |
272
+ | Evidence | 30% | 900 |
273
+ | Options | 25% | 750 |
274
+ | Recommendations | 15% | 450 |
275
+ | Conclusion | 5% | 150 |
276
+
277
+ ---
278
+
279
+ ## Pattern 6: Conference Paper
280
+
281
+ **Best for**: Presenting research in progress or completed studies at academic conferences
282
+ **Typical length**: 2,000-5,000 words (varies by conference)
283
+ **Disciplines**: All
284
+
285
+ ### Structure (Short Paper)
286
+
287
+ ```
288
+ 1. Title, Authors, Affiliations
289
+ 2. Abstract (100-200 words)
290
+ Keywords
291
+ 3. Introduction
292
+ 3.1 Problem and Motivation
293
+ 3.2 Research Question(s)
294
+ 4. Related Work
295
+ 4.1 Key Prior Studies
296
+ 4.2 Gap This Paper Addresses
297
+ 5. Approach / Methodology
298
+ 5.1 Design
299
+ 5.2 Data/Materials
300
+ 5.3 Analysis
301
+ 6. Results (Preliminary or Complete)
302
+ 6.1 Key Findings
303
+ 6.2 Tables/Figures
304
+ 7. Discussion
305
+ 7.1 Interpretation
306
+ 7.2 Limitations
307
+ 8. Conclusion and Future Work
308
+ 9. References
309
+ ```
310
+
311
+ ### Word Allocation (3,000-word example)
312
+ | Section | % | Words |
313
+ |---------|---|-------|
314
+ | Introduction | 15% | 450 |
315
+ | Related Work | 20% | 600 |
316
+ | Methodology | 20% | 600 |
317
+ | Results | 25% | 750 |
318
+ | Discussion | 12% | 360 |
319
+ | Conclusion | 8% | 240 |
320
+
321
+ ## Pattern Selection Guide
322
+
323
+ | If your paper... | Use Pattern |
324
+ |-----------------|-------------|
325
+ | Has original data collection | IMRaD |
326
+ | Synthesizes existing literature | Literature Review |
327
+ | Develops/critiques a theory | Theoretical |
328
+ | Analyzes specific cases in depth | Case Study |
329
+ | Recommends policy actions | Policy Brief |
330
+ | Presents at a conference | Conference Paper |