clearai-dsh 0.3.0 → 0.4.0

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Files changed (148) hide show
  1. package/CHANGELOG.md +147 -0
  2. package/README.md +28 -28
  3. package/README.zh-CN.md +28 -28
  4. package/lib/client.js +861 -2555
  5. package/lib/domain-language.js +552 -48
  6. package/lib/fold.js +351 -1015
  7. package/lib/host.js +47 -557
  8. package/lib/invariant.js +9 -12
  9. package/lib/knowledge-view.js +363 -226
  10. package/lib/lang.js +81 -0
  11. package/package.json +1 -1
  12. package/presets/clearai/agent.cordis.yml +54 -82
  13. package/presets/clearai/clearai.patch.yml +54 -82
  14. package/presets/clearai/plugins/clearai-kernel.js +1590 -5437
  15. package/presets/clearai/plugins/ontology.js +56 -14
  16. package/presets/clearai/plugins/prompts.js +73 -363
  17. package/presets/clearai/skills/clearai-loop/SKILL.md +73 -59
  18. package/presets/clearai/plugins/brain.js +0 -547
  19. package/presets/clearai/plugins/commands.js +0 -199
  20. package/presets/clearai/template/knowledge/README.md +0 -25
  21. package/presets/clearai/template/memory/README.md +0 -34
  22. package/presets/clearai/template/project.md +0 -49
  23. package/presets/clearai/template/skills/README.md +0 -37
  24. package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +0 -43
  25. package/presets/clearai/template/skills/citation-management/SKILL.md +0 -73
  26. package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +0 -908
  27. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +0 -794
  28. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +0 -725
  29. package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +0 -870
  30. package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +0 -839
  31. package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  32. package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +0 -569
  33. package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +0 -349
  34. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +0 -139
  35. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +0 -817
  36. package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +0 -282
  37. package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +0 -398
  38. package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +0 -497
  39. package/presets/clearai/template/skills/data-analysis/SKILL.md +0 -92
  40. package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +0 -23
  41. package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +0 -63
  42. package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -32
  43. package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +0 -12
  44. package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +0 -316
  45. package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +0 -20
  46. package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +0 -30
  47. package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +0 -42
  48. package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +0 -36
  49. package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +0 -25
  50. package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +0 -26
  51. package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +0 -102
  52. package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +0 -62
  53. package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +0 -56
  54. package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -56
  55. package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +0 -13
  56. package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +0 -146
  57. package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +0 -60
  58. package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +0 -41
  59. package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +0 -101
  60. package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +0 -100
  61. package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +0 -194
  62. package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +0 -122
  63. package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +0 -126
  64. package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +0 -152
  65. package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +0 -78
  66. package/presets/clearai/template/skills/domain-presearch/SKILL.md +0 -131
  67. package/presets/clearai/template/skills/domain-presearch/checklists/domain_checklist.md +0 -24
  68. package/presets/clearai/template/skills/domain-presearch/references/figure_code.md +0 -78
  69. package/presets/clearai/template/skills/domain-presearch/references/strategic_frameworks.md +0 -38
  70. package/presets/clearai/template/skills/exploration-loop/SKILL.md +0 -81
  71. package/presets/clearai/template/skills/exploratory-data-analysis/SKILL.md +0 -77
  72. package/presets/clearai/template/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +0 -664
  73. package/presets/clearai/template/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +0 -664
  74. package/presets/clearai/template/skills/exploratory-data-analysis/references/general_scientific_formats.md +0 -518
  75. package/presets/clearai/template/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +0 -620
  76. package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -517
  77. package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -633
  78. package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -547
  79. package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +0 -73
  80. package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -329
  81. package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -198
  82. package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +0 -622
  83. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +0 -139
  84. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +0 -817
  85. package/presets/clearai/template/skills/literature-review/SKILL.md +0 -72
  86. package/presets/clearai/template/skills/literature-review/references/citation_styles.md +0 -166
  87. package/presets/clearai/template/skills/literature-review/references/database_strategies.md +0 -455
  88. package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +0 -176
  89. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +0 -139
  90. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +0 -817
  91. package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +0 -303
  92. package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +0 -221
  93. package/presets/clearai/template/skills/paper-lookup/SKILL.md +0 -59
  94. package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +0 -161
  95. package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +0 -118
  96. package/presets/clearai/template/skills/paper-lookup/references/core.md +0 -150
  97. package/presets/clearai/template/skills/paper-lookup/references/crossref.md +0 -181
  98. package/presets/clearai/template/skills/paper-lookup/references/medrxiv.md +0 -104
  99. package/presets/clearai/template/skills/paper-lookup/references/openalex.md +0 -174
  100. package/presets/clearai/template/skills/paper-lookup/references/pmc.md +0 -152
  101. package/presets/clearai/template/skills/paper-lookup/references/pubmed.md +0 -124
  102. package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +0 -203
  103. package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +0 -127
  104. package/presets/clearai/template/skills/process-presearch/SKILL.md +0 -196
  105. package/presets/clearai/template/skills/process-presearch/checklists/process_checklist.md +0 -18
  106. package/presets/clearai/template/skills/process-presearch/references/figure_code.md +0 -107
  107. package/presets/clearai/template/skills/process-presearch/references/source_attribution_example.md +0 -22
  108. package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +0 -69
  109. package/presets/clearai/template/skills/process-understanding-extraction/checklists/readiness_check.md +0 -34
  110. package/presets/clearai/template/skills/process-understanding-extraction/templates/docx_raw_dump_extractor.py.tpl +0 -132
  111. package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +0 -86
  112. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +0 -89
  113. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief_builder_from_raw_dump.py.tpl +0 -203
  114. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_flow_mermaid.md.tpl +0 -41
  115. package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +0 -53
  116. package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +0 -173
  117. package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +0 -106
  118. package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +0 -64
  119. package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -326
  120. package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +0 -72
  121. package/presets/clearai/template/skills/scientific-critical-thinking/references/common_biases.md +0 -364
  122. package/presets/clearai/template/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -485
  123. package/presets/clearai/template/skills/scientific-critical-thinking/references/experimental_design.md +0 -496
  124. package/presets/clearai/template/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -478
  125. package/presets/clearai/template/skills/scientific-critical-thinking/references/scientific_method.md +0 -169
  126. package/presets/clearai/template/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -506
  127. package/presets/clearai/template/skills/skill-creator/SKILL.md +0 -109
  128. package/presets/clearai/template/skills/skill-creator/references/authoring-guide.md +0 -89
  129. package/presets/clearai/template/skills/statistical-analysis/SKILL.md +0 -79
  130. package/presets/clearai/template/skills/statistical-analysis/references/assumptions_and_diagnostics.md +0 -369
  131. package/presets/clearai/template/skills/statistical-analysis/references/bayesian_statistics.md +0 -653
  132. package/presets/clearai/template/skills/statistical-analysis/references/effect_sizes_and_power.md +0 -578
  133. package/presets/clearai/template/skills/statistical-analysis/references/reporting_standards.md +0 -469
  134. package/presets/clearai/template/skills/statistical-analysis/references/test_selection_guide.md +0 -129
  135. package/presets/clearai/template/skills/statistical-analysis/scripts/assumption_checks.py +0 -538
  136. package/presets/clearai/template/skills/web-artifact/SKILL.md +0 -165
  137. package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.css +0 -229
  138. package/presets/clearai/template/skills/web-artifact/assets/renderer/renderer.js +0 -373
  139. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/LICENSE +0 -263
  140. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/UPSTREAM.md +0 -26
  141. package/presets/clearai/template/skills/web-artifact/assets/vendor/elkjs/elk.bundled.js +0 -6605
  142. package/presets/clearai/template/skills/web-artifact/references/when-drawing-a-topology.md +0 -150
  143. package/presets/clearai/template/skills/web-artifact/references/when-the-page-must-work-offline.md +0 -62
  144. package/presets/clearai/template/skills/web-artifact/scripts/check_artifact.py +0 -167
  145. package/presets/clearai/template/skills/web-artifact/scripts/render_topology.js +0 -272
  146. package/presets/clearai/template/skills/what-if-oracle/LICENSE.txt +0 -5
  147. package/presets/clearai/template/skills/what-if-oracle/SKILL.md +0 -72
  148. package/presets/clearai/template/skills/what-if-oracle/references/scenario-templates.md +0 -154
package/lib/invariant.js CHANGED
@@ -50,9 +50,9 @@ function mutationsOf(event) {
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  }
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52
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  /**
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- * **伪步骤**:目标轴(`goal:<id>`)与世界线轴(`<forkId>:<branchId>`)的裁决也带 `step`,
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- * 但它们本来就不在 `plan/created` 里登记。计划步骤 id 的取字纪律是字母/数字/下划线/短横
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- * (见内核 `STEP_SCHEMA`),两条伪轴一律带冒号。
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+ * **伪步骤**:目标轴(`goal:<id>`)的裁决也带 `step`,但它本来就不在 `plan/created` 里登记。
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+ * 计划步骤 id 的取字纪律是字母/数字/下划线/短横(见内核 `STEP_SCHEMA`),伪轴一律带冒号
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+ * (旧日志里的世界线轴 `<forkId>:<branchId>` 同样带冒号,照旧被识别为伪步骤)。
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  */
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  const isPseudoStep = (step) => String(step).includes(':')
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@@ -84,14 +84,13 @@ function judge(before, mutations, admittedIn, fail) {
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  */
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  const admitted = new Set(admittedIn ?? [])
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  const auditsSeen = new Set((Array.isArray(before?.audits) ? before.audits : []).map((item) => String(item.id)))
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- const scoutsSeen = new Set((Array.isArray(before?.scouts) ? before.scouts : []).map((item) => String(item.id)))
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  for (const mutation of mutations) {
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  if (mutation === null || typeof mutation !== 'object' || typeof mutation.t !== 'string') continue
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  const t = mutation.t
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  const step = mutation.step === undefined || mutation.step === null ? null : String(mutation.step)
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  // ── 契约①:引用完整性(查生产状态,不是另一份索引) ────────────────────
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- if (step !== null && !isPseudoStep(step) && hasAnyStep && ['evidence/recorded', 'observation/recorded', 'step/advanced', 'scout/dispatched'].includes(t)) {
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+ if (step !== null && !isPseudoStep(step) && hasAnyStep && ['evidence/recorded', 'observation/recorded', 'step/advanced'].includes(t)) {
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  if (findStep(before, step) === undefined) fail(`引用完整性:${t} 指向不存在的步骤 ${step}——事实不能指向还没登记的东西`)
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  }
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@@ -105,24 +104,22 @@ function judge(before, mutations, admittedIn, fail) {
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  if (t === 'audit/settled' && !auditsSeen.has(String(mutation.id))) {
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  fail(`结算必有派遣:audit/settled(${String(mutation.id)}) 之前没有 audit/dispatched`)
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  }
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- if (t === 'scout/settled' && !scoutsSeen.has(String(mutation.id))) {
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- fail(`结算必有派遣:scout/settled(${String(mutation.id)}) 之前没有 scout/dispatched`)
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- }
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  if (t === 'audit/dispatched' && mutation.id !== undefined && mutation.id !== null) auditsSeen.add(String(mutation.id))
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- if (t === 'scout/dispatched' && mutation.id !== undefined && mutation.id !== null) scoutsSeen.add(String(mutation.id))
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  // ── 契约④:升格有据(目标登记的门槛 vs 已落账的支持证据) ─────────────────
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  if (t === 'fact/promoted') {
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  const goal = before?.goal ?? null
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  const need = LEVEL_RANK[String(goal?.promote_at_level ?? '')]
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  if (goal !== null && need !== undefined) {
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- /** 顺着 假设(claim 匹配)→ 步骤(tests.hypothesis)→ 证据(support) 这条边走。 */
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+ /** 顺着 假设(claim 匹配)→ 证据(新账写明 hypothesis;旧账走步骤的 tests)→ support 这条边走。 */
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  const hypothesis = (Array.isArray(before?.hypotheses) ? before.hypotheses : []).find((item) => String(item.claim ?? '') === String(mutation.text ?? ''))
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  const hypId = hypothesis === undefined ? null : String(hypothesis.id)
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  const stepIds = new Set(
123
- hypId === null ? [] : plans.flatMap((plan) => (plan.steps ?? []).filter((s) => String(s?.tests?.hypothesis ?? '') === hypId).map((s) => String(s.id))),
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+ hypId === null ? [] : plans.flatMap((plan) => (plan.steps ?? []).filter((s) => (s?.tests?.hypotheses ?? []).map(String).includes(hypId)).map((s) => String(s.id))),
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+ )
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+ const support = (Array.isArray(before?.evidence) ? before.evidence : []).filter(
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+ (item) => String(item.verdict) === 'support' && (hypId === null || (item.hypothesis !== undefined ? String(item.hypothesis) === hypId : stepIds.has(String(item.step)))),
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  )
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- const support = (Array.isArray(before?.evidence) ? before.evidence : []).filter((item) => String(item.verdict) === 'support' && (hypId === null || stepIds.has(String(item.step))))
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  const best = support.reduce((max, item) => Math.max(max, LEVEL_RANK[String(item.level)] ?? -1), -1)
127
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  if (best < need) fail(`升格有据:fact/promoted 的最高支持等级(${best === -1 ? '无' : `L${best}`})没到目标登记的 promote_at_level(${String(goal.promote_at_level)})`)
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  }