scientify 1.13.5 → 1.13.6

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Files changed (35) hide show
  1. package/dist/src/hooks/research-mode.d.ts.map +1 -1
  2. package/dist/src/hooks/research-mode.js +30 -1
  3. package/dist/src/hooks/research-mode.js.map +1 -1
  4. package/dist/src/knowledge-state/render.d.ts.map +1 -1
  5. package/dist/src/knowledge-state/render.js +29 -0
  6. package/dist/src/knowledge-state/render.js.map +1 -1
  7. package/dist/src/knowledge-state/store.d.ts.map +1 -1
  8. package/dist/src/knowledge-state/store.js +216 -0
  9. package/dist/src/knowledge-state/store.js.map +1 -1
  10. package/dist/src/knowledge-state/types.d.ts +7 -0
  11. package/dist/src/knowledge-state/types.d.ts.map +1 -1
  12. package/dist/src/literature/subscription-state.d.ts.map +1 -1
  13. package/dist/src/literature/subscription-state.js +184 -8
  14. package/dist/src/literature/subscription-state.js.map +1 -1
  15. package/dist/src/research-subscriptions/handlers.d.ts.map +1 -1
  16. package/dist/src/research-subscriptions/handlers.js +11 -1
  17. package/dist/src/research-subscriptions/handlers.js.map +1 -1
  18. package/dist/src/research-subscriptions/parse.d.ts.map +1 -1
  19. package/dist/src/research-subscriptions/parse.js +15 -0
  20. package/dist/src/research-subscriptions/parse.js.map +1 -1
  21. package/dist/src/research-subscriptions/prompt.d.ts +1 -1
  22. package/dist/src/research-subscriptions/prompt.d.ts.map +1 -1
  23. package/dist/src/research-subscriptions/prompt.js +66 -12
  24. package/dist/src/research-subscriptions/prompt.js.map +1 -1
  25. package/dist/src/research-subscriptions/types.d.ts +1 -0
  26. package/dist/src/research-subscriptions/types.d.ts.map +1 -1
  27. package/dist/src/tools/scientify-cron.d.ts +2 -0
  28. package/dist/src/tools/scientify-cron.d.ts.map +1 -1
  29. package/dist/src/tools/scientify-cron.js +88 -5
  30. package/dist/src/tools/scientify-cron.js.map +1 -1
  31. package/dist/src/tools/scientify-literature-state.d.ts +14 -0
  32. package/dist/src/tools/scientify-literature-state.d.ts.map +1 -1
  33. package/dist/src/tools/scientify-literature-state.js +51 -0
  34. package/dist/src/tools/scientify-literature-state.js.map +1 -1
  35. package/package.json +1 -1
package/dist/src/hooks/research-mode.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AA0EF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,SAAS,WAAW,KAAG,UAAU,CAO7D"}
1
+ {"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAkGF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,SAAS,WAAW,KAAG,UAAU,CAe7D"}
package/dist/src/hooks/research-mode.js CHANGED
@@ -24,6 +24,9 @@ Scheduling:
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  - If user asks "create/start a research task and run now, then return raw status JSON",
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  call \`scientify_cron_job\` with \`action=upsert\` + \`run_now=true\` and return \`status_json\` from tool output.
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  Do not emulate this with hand-written JSON.
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+ - Treat \`status_json\` as the single source of truth for run result and hypothesis persistence.
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+ Never claim "hypothesis generated/persisted" unless \`status_json.knowledge_state_summary.hypothesis_gate.accepted > 0\`
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+ and \`status_json.recent_hypotheses\` is non-empty.
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  Execution truth:
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  - Do not claim background progress unless you created a real async handle (job_id/task_id).
@@ -41,10 +44,18 @@ Run profile defaults:
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  Research quality and gating:
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  - Full-text-first for core evidence papers.
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  - If full text unavailable: set full_text_read=false and unread_reason.
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+ - Adaptive retrieval intent:
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+ * early cycles: prioritize foundational/survey papers to establish field map
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+ * later cycles: expand into mainstream variants and adjacent tracks
50
+ * when a hypothesis appears: immediately run one validation follow-up (supporting + critical evidence), do not wait for next heartbeat
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  - In core paper notes, avoid placeholders ("N/A", "not provided", "unknown"); either provide concrete content or omit field.
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  - Evidence binding for key conclusions should include section + locator + quote.
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  - BRIDGE requires resolvable evidence_ids and at least one full-text-backed evidence source.
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  - If BRIDGE, NEW+REVISE, or unread core backlog appears, execute one reflection follow-up query and persist trace/result.
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+ - If a cycle is empty, do not stop at "no papers":
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+ * diagnose whether it is query/alias/recency mismatch vs scope saturation
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+ * persist diagnosis and next-query/pivot hints in run_log notes
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+ * keep topic continuity, but prepare adjacent sub-direction queries that serve current idea validation
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  - Hypotheses are accepted only when evidence_ids and dependency_path are sufficient; otherwise reject via hypothesis_gate reasons.
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  - Before user-facing wording, check latest status.hypothesis_gate.accepted:
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  * accepted == 0: factual report only; do not output speculative "next high-value routes"/"deep dive" guidance.
@@ -68,6 +79,15 @@ Do not call scientify_cron_job (or create another cron job) from this run.
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  Do not recursively schedule run_now from within cron.
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  Use the existing execution handle and complete prepare -> record -> status directly.
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  If workload is too heavy for this turn, prefer sessions_spawn task delegation (with task id) instead of nested cron.`;
82
+ const FORCE_ZH_RE = /output language:\s*chinese|chinese \(simplified\)|必须使用中文回复|请用中文|用中文输出|中文回复/iu;
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+ const FORCE_EN_RE = /output language:\s*english|please use english|use english|英文回复|请用英文/iu;
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+ const LANGUAGE_PROMPT_ZH = `[Language]
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+ You must reply in Simplified Chinese for all user-facing content.
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+ If you are about to respond in English, translate to Chinese and output only Chinese.
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+ `;
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+ const LANGUAGE_PROMPT_EN = `[Language]
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+ You must reply in English for all user-facing content unless quoting sources.
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+ `;
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  /**
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  * Injects on every prompt build (survives compaction).
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  */
@@ -75,8 +95,17 @@ export function createResearchModeHook() {
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  return (_event, context) => {
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  const sessionKey = typeof context.sessionKey === "string" ? context.sessionKey : "";
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  const inCronContext = sessionKey.includes(":cron:");
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+ const promptText = typeof _event.prompt === "string" ? _event.prompt : "";
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+ let languagePrefix = "";
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+ if (FORCE_EN_RE.test(promptText)) {
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+ languagePrefix = LANGUAGE_PROMPT_EN;
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+ }
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+ else if (FORCE_ZH_RE.test(promptText)) {
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+ languagePrefix = LANGUAGE_PROMPT_ZH;
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+ }
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+ const basePrompt = inCronContext ? `${RESEARCH_MODE_PROMPT}\n${CRON_CONTEXT_GUARD}` : RESEARCH_MODE_PROMPT;
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  return {
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- prependContext: inCronContext ? `${RESEARCH_MODE_PROMPT}\n${CRON_CONTEXT_GUARD}` : RESEARCH_MODE_PROMPT,
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+ prependContext: languagePrefix ? `${languagePrefix}\n${basePrompt}` : basePrompt,
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  };
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  };
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  }
package/dist/src/hooks/research-mode.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"research-mode.js","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAmBA;;GAEG;AACH,MAAM,oBAAoB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6EAsEgD,CAAC;AAE9E,MAAM,kBAAkB,GAAG;;;;;;qHAM0F,CAAC;AAEtH,MAAM,WAAW,GACf,8EAA8E,CAAC;AACjF,MAAM,WAAW,GAAG,uEAAuE,CAAC;AAE5F,MAAM,kBAAkB,GAAG;;;CAG1B,CAAC;AAEF,MAAM,kBAAkB,GAAG;;CAE1B,CAAC;AAEF;;GAEG;AACH,MAAM,UAAU,sBAAsB;IACpC,OAAO,CAAC,MAAiB,EAAE,OAAoB,EAAc,EAAE;QAC7D,MAAM,UAAU,GAAG,OAAO,OAAO,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;QACpF,MAAM,aAAa,GAAG,UAAU,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;QACpD,MAAM,UAAU,GAAG,OAAO,MAAM,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;QAC1E,IAAI,cAAc,GAAG,EAAE,CAAC;QACxB,IAAI,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;YACjC,cAAc,GAAG,kBAAkB,CAAC;QACtC,CAAC;aAAM,IAAI,WAAW,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,CAAC;YACxC,cAAc,GAAG,kBAAkB,CAAC;QACtC,CAAC;QACD,MAAM,UAAU,GAAG,aAAa,CAAC,CAAC,CAAC,GAAG,oBAAoB,KAAK,kBAAkB,EAAE,CAAC,CAAC,CAAC,oBAAoB,CAAC;QAC3G,OAAO;YACL,cAAc,EAAE,cAAc,CAAC,CAAC,CAAC,GAAG,cAAc,KAAK,UAAU,EAAE,CAAC,CAAC,CAAC,UAAU;SACjF,CAAC;IACJ,CAAC,CAAC;AACJ,CAAC"}
package/dist/src/knowledge-state/render.d.ts.map CHANGED
@@ -1 +1 @@
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package/dist/src/knowledge-state/render.js CHANGED
@@ -392,11 +392,40 @@ export function renderHypothesisMarkdown(args) {
392
392
  "## Statement",
393
393
  args.hypothesis.statement,
394
394
  "",
395
+ "## Problem Gap",
396
+ args.hypothesis.problemGap ?? "pending",
397
+ "",
398
+ "## Proposed Mechanism",
399
+ args.hypothesis.proposedMechanism ?? "pending",
400
+ "",
401
+ "## Novelty Rationale",
402
+ args.hypothesis.noveltyRationale ?? "pending",
403
+ "",
395
404
  "## Dependency Path",
396
405
  ...(args.hypothesis.dependencyPath && args.hypothesis.dependencyPath.length > 0
397
406
  ? args.hypothesis.dependencyPath.map((step, idx) => `${idx + 1}. ${step}`)
398
407
  : ["- Pending enrichment: dependency path not extracted in this run."]),
399
408
  "",
409
+ "## Falsifiable Predictions",
410
+ ...(args.hypothesis.falsifiablePredictions && args.hypothesis.falsifiablePredictions.length > 0
411
+ ? args.hypothesis.falsifiablePredictions.map((item, idx) => `${idx + 1}. ${item}`)
412
+ : ["1. (none)"]),
413
+ "",
414
+ "## Critical Assumptions",
415
+ ...(args.hypothesis.criticalAssumptions && args.hypothesis.criticalAssumptions.length > 0
416
+ ? args.hypothesis.criticalAssumptions.map((item, idx) => `${idx + 1}. ${item}`)
417
+ : ["1. (none)"]),
418
+ "",
419
+ "## Failure Modes",
420
+ ...(args.hypothesis.failureModes && args.hypothesis.failureModes.length > 0
421
+ ? args.hypothesis.failureModes.map((item, idx) => `${idx + 1}. ${item}`)
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+ : ["1. (none)"]),
423
+ "",
424
+ "## Success Criteria",
425
+ ...(args.hypothesis.successCriteria && args.hypothesis.successCriteria.length > 0
426
+ ? args.hypothesis.successCriteria.map((item, idx) => `${idx + 1}. ${item}`)
427
+ : ["1. (none)"]),
428
+ "",
400
429
  "## Strengths",
401
430
  ...(args.hypothesis.strengths && args.hypothesis.strengths.length > 0
402
431
  ? args.hypothesis.strengths.map((item, idx) => `${idx + 1}. ${item}`)
package/dist/src/knowledge-state/render.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/src/knowledge-state/store.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"store.d.ts","sourceRoot":"","sources":["../../../src/knowledge-state/store.ts"],"names":[],"mappings":"AAkBA,OAAO,KAAK,EACV,uBAAuB,EAQvB,qBAAqB,EAOtB,MAAM,YAAY,CAAC;AA4kDpB,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,uBAAuB,GAAG,OAAO,CAAC;IAChF,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,qBAAqB,CAAC;IAC/B,KAAK,EAAE,MAAM,CAAC;IACd,cAAc,EAAE,OAAO,CAAC;CACzB,CAAC,CAibD;AAED,wBAAsB,oBAAoB,CAAC,IAAI,EAAE;IAC/C,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,qBAAqB,CAAA;CAAE,GAAG,SAAS,CAAC,CA0BhG"}
1
+ {"version":3,"file":"store.d.ts","sourceRoot":"","sources":["../../../src/knowledge-state/store.ts"],"names":[],"mappings":"AAkBA,OAAO,KAAK,EACV,uBAAuB,EAQvB,qBAAqB,EAOtB,MAAM,YAAY,CAAC;AA+tDpB,wBAAsB,kBAAkB,CAAC,KAAK,EAAE,uBAAuB,GAAG,OAAO,CAAC;IAChF,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,qBAAqB,CAAC;IAC/B,KAAK,EAAE,MAAM,CAAC;IACd,cAAc,EAAE,OAAO,CAAC;CACzB,CAAC,CA4gBD;AAED,wBAAsB,oBAAoB,CAAC,IAAI,EAAE;IAC/C,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB,GAAG,OAAO,CAAC;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,qBAAqB,CAAA;CAAE,GAAG,SAAS,CAAC,CA0BhG"}
package/dist/src/knowledge-state/store.js CHANGED
@@ -24,6 +24,10 @@ const MIN_HYPOTHESIS_STATEMENT_CHARS = 48;
24
24
  const MIN_HYPOTHESIS_STRENGTHS = 2;
25
25
  const MIN_HYPOTHESIS_WEAKNESSES = 2;
26
26
  const MIN_HYPOTHESIS_PLAN_STEPS = 3;
27
+ const MIN_HYPOTHESIS_PREDICTIONS = 2;
28
+ const MIN_HYPOTHESIS_ASSUMPTIONS = 2;
29
+ const MIN_HYPOTHESIS_FAILURE_MODES = 1;
30
+ const MIN_HYPOTHESIS_SUCCESS_CRITERIA = 2;
27
31
  const MIN_HYPOTHESIS_STRICT_ACCEPT_SCORE = 70;
28
32
  const MIN_HYPOTHESIS_ACCEPT_SELF_SCORE_AVG = 3.2;
29
33
  const PLACEHOLDER_TEXT_RE = /^(?:n\/a|na|none|not provided|not available|unknown|tbd|todo|null|nil|未提供|暂无|未知|无)$/iu;
@@ -130,6 +134,7 @@ async function ensureLayout(projectPath) {
130
134
  await mkdir(path.join(root, "paper_notes"), { recursive: true });
131
135
  await mkdir(path.join(root, "daily_changes"), { recursive: true });
132
136
  await mkdir(path.join(root, "hypotheses"), { recursive: true });
137
+ await mkdir(path.join(root, "hypotheses", "rejected"), { recursive: true });
133
138
  await mkdir(path.join(root, "logs"), { recursive: true });
134
139
  }
135
140
  async function loadState(projectPath) {
@@ -1046,6 +1051,17 @@ function deriveReflectionTasks(args) {
1046
1051
  status: queryMatchesTrace(query, args.trace) ? "executed" : "planned",
1047
1052
  });
1048
1053
  }
1054
+ if (tasks.length === 0 && args.corePapers.length === 0 && args.changes.length === 0) {
1055
+ const query = buildReflectionQuery(args.topic, `${args.topic} survey review foundational mainstream variants`, "empty cycle diagnosis");
1056
+ tasks.push({
1057
+ id: sanitizeId(`empty-cycle-${query}`),
1058
+ trigger: "TREND",
1059
+ reason: "No new core papers found in this cycle. Re-check query scope/time window and expand to adjacent sub-directions for idea support or criticism.",
1060
+ query,
1061
+ priority: "medium",
1062
+ status: queryMatchesTrace(query, args.trace) ? "executed" : "planned",
1063
+ });
1064
+ }
1049
1065
  const dedup = new Map();
1050
1066
  for (const task of tasks) {
1051
1067
  const key = normalizeText(task.query).toLowerCase();
@@ -1110,6 +1126,7 @@ function sanitizeKnowledgeChanges(args) {
1110
1126
  }
1111
1127
  function applyHypothesisGate(args) {
1112
1128
  const acceptedHypotheses = [];
1129
+ const audits = [];
1113
1130
  const rejectionReasonSet = new Set();
1114
1131
  const paperLookup = buildPaperLookup(args.allRunPapers);
1115
1132
  const fullTextEvidenceIds = uniqueText(args.allRunPapers
@@ -1158,6 +1175,31 @@ function applyHypothesisGate(args) {
1158
1175
  if (dependencyPathLength < MIN_HYPOTHESIS_DEPENDENCY_STEPS) {
1159
1176
  reasons.push(`dependency_path_too_short(${dependencyPathLength}<${MIN_HYPOTHESIS_DEPENDENCY_STEPS})`);
1160
1177
  }
1178
+ if (!hypothesis.problemGap || normalizeText(hypothesis.problemGap).length < 24) {
1179
+ reasons.push("problem_gap_missing_or_too_short");
1180
+ }
1181
+ if (!hypothesis.proposedMechanism || normalizeText(hypothesis.proposedMechanism).length < 24) {
1182
+ reasons.push("proposed_mechanism_missing_or_too_short");
1183
+ }
1184
+ if (!hypothesis.noveltyRationale || normalizeText(hypothesis.noveltyRationale).length < 24) {
1185
+ reasons.push("novelty_rationale_missing_or_too_short");
1186
+ }
1187
+ const predictionCount = hypothesis.falsifiablePredictions?.length ?? 0;
1188
+ if (predictionCount < MIN_HYPOTHESIS_PREDICTIONS) {
1189
+ reasons.push(`predictions_too_few(${predictionCount}<${MIN_HYPOTHESIS_PREDICTIONS})`);
1190
+ }
1191
+ const assumptionCount = hypothesis.criticalAssumptions?.length ?? 0;
1192
+ if (assumptionCount < MIN_HYPOTHESIS_ASSUMPTIONS) {
1193
+ reasons.push(`assumptions_too_few(${assumptionCount}<${MIN_HYPOTHESIS_ASSUMPTIONS})`);
1194
+ }
1195
+ const failureModeCount = hypothesis.failureModes?.length ?? 0;
1196
+ if (failureModeCount < MIN_HYPOTHESIS_FAILURE_MODES) {
1197
+ reasons.push(`failure_modes_too_few(${failureModeCount}<${MIN_HYPOTHESIS_FAILURE_MODES})`);
1198
+ }
1199
+ const successCriteriaCount = hypothesis.successCriteria?.length ?? 0;
1200
+ if (successCriteriaCount < MIN_HYPOTHESIS_SUCCESS_CRITERIA) {
1201
+ reasons.push(`success_criteria_too_few(${successCriteriaCount}<${MIN_HYPOTHESIS_SUCCESS_CRITERIA})`);
1202
+ }
1161
1203
  const strengthsCount = hypothesis.strengths?.length ?? 0;
1162
1204
  if (strengthsCount < MIN_HYPOTHESIS_STRENGTHS) {
1163
1205
  reasons.push(`strengths_too_few(${strengthsCount}<${MIN_HYPOTHESIS_STRENGTHS})`);
@@ -1221,6 +1263,13 @@ function applyHypothesisGate(args) {
1221
1263
  };
1222
1264
  const isRepairableReason = (reason) => {
1223
1265
  return (reason.startsWith("dependency_path_too_short(") ||
1266
+ reason === "problem_gap_missing_or_too_short" ||
1267
+ reason === "proposed_mechanism_missing_or_too_short" ||
1268
+ reason === "novelty_rationale_missing_or_too_short" ||
1269
+ reason.startsWith("predictions_too_few(") ||
1270
+ reason.startsWith("assumptions_too_few(") ||
1271
+ reason.startsWith("failure_modes_too_few(") ||
1272
+ reason.startsWith("success_criteria_too_few(") ||
1224
1273
  reason.startsWith("strengths_too_few(") ||
1225
1274
  reason.startsWith("weaknesses_too_few(") ||
1226
1275
  reason.startsWith("plan_steps_too_few(") ||
@@ -1241,7 +1290,14 @@ function applyHypothesisGate(args) {
1241
1290
  return undefined;
1242
1291
  const revised = {
1243
1292
  ...hypothesis,
1293
+ ...(hypothesis.problemGap ? { problemGap: hypothesis.problemGap } : {}),
1294
+ ...(hypothesis.proposedMechanism ? { proposedMechanism: hypothesis.proposedMechanism } : {}),
1295
+ ...(hypothesis.noveltyRationale ? { noveltyRationale: hypothesis.noveltyRationale } : {}),
1244
1296
  ...(hypothesis.dependencyPath ? { dependencyPath: [...hypothesis.dependencyPath] } : {}),
1297
+ ...(hypothesis.falsifiablePredictions ? { falsifiablePredictions: [...hypothesis.falsifiablePredictions] } : {}),
1298
+ ...(hypothesis.criticalAssumptions ? { criticalAssumptions: [...hypothesis.criticalAssumptions] } : {}),
1299
+ ...(hypothesis.failureModes ? { failureModes: [...hypothesis.failureModes] } : {}),
1300
+ ...(hypothesis.successCriteria ? { successCriteria: [...hypothesis.successCriteria] } : {}),
1245
1301
  ...(hypothesis.strengths ? { strengths: [...hypothesis.strengths] } : {}),
1246
1302
  ...(hypothesis.weaknesses ? { weaknesses: [...hypothesis.weaknesses] } : {}),
1247
1303
  ...(hypothesis.planSteps ? { planSteps: [...hypothesis.planSteps] } : {}),
@@ -1263,6 +1319,58 @@ function applyHypothesisGate(args) {
1263
1319
  ];
1264
1320
  changed = true;
1265
1321
  }
1322
+ if (!revised.problemGap || normalizeText(revised.problemGap).length < 24) {
1323
+ revised.problemGap =
1324
+ "Current literature shows evidence signals, but no validated design rule translates these signals into a reproducible intervention.";
1325
+ changed = true;
1326
+ }
1327
+ if (!revised.proposedMechanism || normalizeText(revised.proposedMechanism).length < 24) {
1328
+ revised.proposedMechanism =
1329
+ "Use evidence-linked control variables to adapt method configuration online, then verify whether the control action improves target metrics under fixed budget.";
1330
+ changed = true;
1331
+ }
1332
+ if (!revised.noveltyRationale || normalizeText(revised.noveltyRationale).length < 24) {
1333
+ revised.noveltyRationale =
1334
+ "Prior work reports signals independently; this hypothesis couples them into one executable control rule with explicit falsification conditions.";
1335
+ changed = true;
1336
+ }
1337
+ while ((revised.falsifiablePredictions?.length ?? 0) < MIN_HYPOTHESIS_PREDICTIONS) {
1338
+ const idx = revised.falsifiablePredictions?.length ?? 0;
1339
+ revised.falsifiablePredictions = [
1340
+ ...(revised.falsifiablePredictions ?? []),
1341
+ idx === 0
1342
+ ? "If the proposed mechanism is valid, primary metric improves versus fixed baseline under matched budget."
1343
+ : "If mechanism signal is ablated, improvement should disappear or significantly shrink.",
1344
+ ];
1345
+ changed = true;
1346
+ }
1347
+ while ((revised.criticalAssumptions?.length ?? 0) < MIN_HYPOTHESIS_ASSUMPTIONS) {
1348
+ const idx = revised.criticalAssumptions?.length ?? 0;
1349
+ revised.criticalAssumptions = [
1350
+ ...(revised.criticalAssumptions ?? []),
1351
+ idx === 0
1352
+ ? "Evidence signals remain stable enough across runs to drive adaptation decisions."
1353
+ : "Evaluation datasets and task settings reflect the intended deployment regime.",
1354
+ ];
1355
+ changed = true;
1356
+ }
1357
+ while ((revised.failureModes?.length ?? 0) < MIN_HYPOTHESIS_FAILURE_MODES) {
1358
+ revised.failureModes = [
1359
+ ...(revised.failureModes ?? []),
1360
+ "Signal noise or distribution shift causes unstable control actions and nullifies expected gains.",
1361
+ ];
1362
+ changed = true;
1363
+ }
1364
+ while ((revised.successCriteria?.length ?? 0) < MIN_HYPOTHESIS_SUCCESS_CRITERIA) {
1365
+ const idx = revised.successCriteria?.length ?? 0;
1366
+ revised.successCriteria = [
1367
+ ...(revised.successCriteria ?? []),
1368
+ idx === 0
1369
+ ? "Primary metric improves by a pre-registered margin against strongest baseline under matched compute."
1370
+ : "At least one ablation confirms the claimed mechanism rather than incidental tuning effects.",
1371
+ ];
1372
+ changed = true;
1373
+ }
1266
1374
  while ((revised.strengths?.length ?? 0) < MIN_HYPOTHESIS_STRENGTHS) {
1267
1375
  revised.strengths = [
1268
1376
  ...(revised.strengths ?? []),
@@ -1327,6 +1435,12 @@ function applyHypothesisGate(args) {
1327
1435
  const firstReasons = evaluateHypothesisReasons(hypothesis);
1328
1436
  if (firstReasons.length === 0) {
1329
1437
  acceptedHypotheses.push(hypothesis);
1438
+ audits.push({
1439
+ hypothesis,
1440
+ accepted: true,
1441
+ reasons: [],
1442
+ autoRevised: false,
1443
+ });
1330
1444
  continue;
1331
1445
  }
1332
1446
  const autoRevised = autoReviseHypothesis(hypothesis, firstReasons);
@@ -1334,14 +1448,32 @@ function applyHypothesisGate(args) {
1334
1448
  const secondReasons = evaluateHypothesisReasons(autoRevised);
1335
1449
  if (secondReasons.length === 0) {
1336
1450
  acceptedHypotheses.push(autoRevised);
1451
+ audits.push({
1452
+ hypothesis: autoRevised,
1453
+ accepted: true,
1454
+ reasons: [],
1455
+ autoRevised: true,
1456
+ });
1337
1457
  continue;
1338
1458
  }
1459
+ audits.push({
1460
+ hypothesis: autoRevised,
1461
+ accepted: false,
1462
+ reasons: secondReasons,
1463
+ autoRevised: true,
1464
+ });
1339
1465
  for (const reason of secondReasons)
1340
1466
  rejectionReasonSet.add(reason);
1341
1467
  continue;
1342
1468
  }
1343
1469
  const reasons = firstReasons;
1344
1470
  if (reasons.length > 0) {
1471
+ audits.push({
1472
+ hypothesis,
1473
+ accepted: false,
1474
+ reasons,
1475
+ autoRevised: false,
1476
+ });
1345
1477
  for (const reason of reasons)
1346
1478
  rejectionReasonSet.add(reason);
1347
1479
  continue;
@@ -1349,6 +1481,7 @@ function applyHypothesisGate(args) {
1349
1481
  }
1350
1482
  return {
1351
1483
  acceptedHypotheses,
1484
+ audits,
1352
1485
  gate: {
1353
1486
  accepted: acceptedHypotheses.length,
1354
1487
  rejected: Math.max(0, args.hypotheses.length - acceptedHypotheses.length),
@@ -1516,6 +1649,8 @@ export async function commitKnowledgeRun(input) {
1516
1649
  const knowledgeDir = path.join(rootPath, "knowledge");
1517
1650
  const paperNotesDir = path.join(rootPath, "paper_notes");
1518
1651
  const hypothesesDir = path.join(rootPath, "hypotheses");
1652
+ const rejectedHypothesesDir = path.join(hypothesesDir, "rejected");
1653
+ await mkdir(rejectedHypothesesDir, { recursive: true });
1519
1654
  await appendMarkdown(path.join(logDir, `day-${dayKey}-ingest.md`), renderIngestLogMarkdown({ now: nowIso, runId, scope: stream.scope, topic: stream.topic, papers: corePapers }));
1520
1655
  await appendMarkdown(path.join(logDir, `day-${dayKey}-exploration.md`), renderExplorationLogMarkdown({
1521
1656
  now: nowIso,
@@ -1621,7 +1756,9 @@ export async function commitKnowledgeRun(input) {
1621
1756
  }
1622
1757
  stream.paperNotes = [...new Set([...runPaperNoteFiles, ...stream.paperNotes])].slice(0, MAX_PAPER_NOTES);
1623
1758
  const recentHypothesisSummaries = [];
1759
+ const rejectedHypothesisArtifacts = [];
1624
1760
  let seq = stream.totalHypotheses;
1761
+ let rejectedSeq = 0;
1625
1762
  const dayToken = dayKey.replace(/-/g, "");
1626
1763
  for (const hypothesis of acceptedHypotheses) {
1627
1764
  seq += 1;
@@ -1642,6 +1779,82 @@ export async function commitKnowledgeRun(input) {
1642
1779
  : {}),
1643
1780
  });
1644
1781
  }
1782
+ for (const audit of hypothesisEval.audits.filter((item) => !item.accepted)) {
1783
+ rejectedSeq += 1;
1784
+ const sanitizedSourceId = sanitizeId(audit.hypothesis.id ?? "");
1785
+ const hypothesisId = sanitizedSourceId.length > 0
1786
+ ? `${sanitizedSourceId}-rejected`
1787
+ : `hyp-${dayToken}-${String(rejectedSeq).padStart(4, "0")}-rejected`;
1788
+ const file = `${hypothesisId}.md`;
1789
+ const evidenceLines = audit.hypothesis.evidenceIds && audit.hypothesis.evidenceIds.length > 0
1790
+ ? audit.hypothesis.evidenceIds.map((id, idx) => `${idx + 1}. ${id}`)
1791
+ : ["1. (none)"];
1792
+ const dependencyLines = audit.hypothesis.dependencyPath && audit.hypothesis.dependencyPath.length > 0
1793
+ ? audit.hypothesis.dependencyPath.map((item, idx) => `${idx + 1}. ${item}`)
1794
+ : ["1. (none)"];
1795
+ const reasons = audit.reasons.length > 0 ? audit.reasons : ["rejected_without_reason"];
1796
+ const content = [
1797
+ `# ${hypothesisId}`,
1798
+ "",
1799
+ `- Run: ${runId}`,
1800
+ "- Gate Decision: rejected",
1801
+ `- Auto Revised: ${audit.autoRevised ? "yes" : "no"}`,
1802
+ "",
1803
+ "## Rejection Reasons",
1804
+ ...reasons.map((reason, idx) => `${idx + 1}. ${reason}`),
1805
+ "",
1806
+ "## Statement",
1807
+ audit.hypothesis.statement,
1808
+ "",
1809
+ "## Problem Gap",
1810
+ audit.hypothesis.problemGap ?? "pending",
1811
+ "",
1812
+ "## Proposed Mechanism",
1813
+ audit.hypothesis.proposedMechanism ?? "pending",
1814
+ "",
1815
+ "## Novelty Rationale",
1816
+ audit.hypothesis.noveltyRationale ?? "pending",
1817
+ "",
1818
+ "## Trigger",
1819
+ audit.hypothesis.trigger,
1820
+ "",
1821
+ "## Evidence IDs",
1822
+ ...evidenceLines,
1823
+ "",
1824
+ "## Dependency Path",
1825
+ ...dependencyLines,
1826
+ "",
1827
+ "## Falsifiable Predictions",
1828
+ ...(audit.hypothesis.falsifiablePredictions && audit.hypothesis.falsifiablePredictions.length > 0
1829
+ ? audit.hypothesis.falsifiablePredictions.map((item, idx) => `${idx + 1}. ${item}`)
1830
+ : ["1. (none)"]),
1831
+ "",
1832
+ "## Critical Assumptions",
1833
+ ...(audit.hypothesis.criticalAssumptions && audit.hypothesis.criticalAssumptions.length > 0
1834
+ ? audit.hypothesis.criticalAssumptions.map((item, idx) => `${idx + 1}. ${item}`)
1835
+ : ["1. (none)"]),
1836
+ "",
1837
+ "## Failure Modes",
1838
+ ...(audit.hypothesis.failureModes && audit.hypothesis.failureModes.length > 0
1839
+ ? audit.hypothesis.failureModes.map((item, idx) => `${idx + 1}. ${item}`)
1840
+ : ["1. (none)"]),
1841
+ "",
1842
+ "## Success Criteria",
1843
+ ...(audit.hypothesis.successCriteria && audit.hypothesis.successCriteria.length > 0
1844
+ ? audit.hypothesis.successCriteria.map((item, idx) => `${idx + 1}. ${item}`)
1845
+ : ["1. (none)"]),
1846
+ "",
1847
+ "> Persisted for traceability. This hypothesis did not pass hypothesis_gate in this run.",
1848
+ "",
1849
+ ].join("\n");
1850
+ await writeFile(path.join(rejectedHypothesesDir, file), content, "utf-8");
1851
+ rejectedHypothesisArtifacts.push({
1852
+ id: hypothesisId,
1853
+ file: path.join("rejected", file),
1854
+ reasons: reasons.slice(0, MAX_HYPOTHESIS_REJECTION_REASONS),
1855
+ autoRevised: audit.autoRevised,
1856
+ });
1857
+ }
1645
1858
  const fullTextStats = countFullTextStats(mergedRunPapers);
1646
1859
  const structuredProfileCount = mergedRunPapers.filter(hasStructuredProfile).length;
1647
1860
  await writeFile(path.join(knowledgeDir, "_index.md"), renderKnowledgeIndexMarkdown({
@@ -1709,6 +1922,7 @@ export async function commitKnowledgeRun(input) {
1709
1922
  hypotheses: acceptedHypotheses,
1710
1923
  submittedHypotheses,
1711
1924
  hypothesisGate: hypothesisEval.gate,
1925
+ rejectedHypothesisArtifacts,
1712
1926
  paperNoteFiles: runPaperNoteFiles,
1713
1927
  quality: {
1714
1928
  fullTextReadCount: fullTextStats.fullTextReadCount,
@@ -1747,7 +1961,9 @@ export async function commitKnowledgeRun(input) {
1747
1961
  droppedBridgeCount: changeSanitization.droppedBridgeCount,
1748
1962
  hypothesisCount: recentHypothesisSummaries.length,
1749
1963
  submittedHypothesisCount: submittedHypotheses.length,
1964
+ rejectedHypothesisCount: rejectedHypothesisArtifacts.length,
1750
1965
  hypothesisGate: hypothesisEval.gate,
1966
+ rejectedHypothesisArtifacts,
1751
1967
  triggerState: stream.triggerState,
1752
1968
  reflectionTasks,
1753
1969
  corePapers,