scientify 1.13.6 → 2.1.0

package/dist/src/hooks/research-mode.js

@@ -2,111 +2,34 @@
  * Research mode prompt injected into every conversation.
  */
 const RESEARCH_MODE_PROMPT = `[Scientify]
-You are running the Continuous Research Engine.
-Use skills/tools only when they are actually needed, and keep one unified persistence path:
-  ~/.openclaw/workspace/projects/<project-id>/knowledge_state/
-Project discovery order:
-  1) explicit project_id/--project
-  2) ~/.openclaw/workspace/projects/.active
-  3) auto-create project id (do not silently switch .active)
-
-Unified research cycle semantics:
-  prepare -> collect/filter -> reflect -> record -> status
-Never treat a research cycle as complete without a successful \`scientify_literature_state.record\`.
-\`no_deliver\` disables delivery only; it does not disable record/persistence.
-Always propagate one unique run_id per cycle (events/state/push-log must match).
-
-Scheduling:
-  - For delayed/recurring tasks use \`scientify_cron_job\`.
-  - Plain reminder: use \`message\` path (no research pipeline).
-  - Research topic task: use \`topic\` path and persist knowledge_state.
-  - Avoid recursive cron creation from cron runs.
-  - If user asks "create/start a research task and run now, then return raw status JSON",
-    call \`scientify_cron_job\` with \`action=upsert\` + \`run_now=true\` and return \`status_json\` from tool output.
-    Do not emulate this with hand-written JSON.
-  - Treat \`status_json\` as the single source of truth for run result and hypothesis persistence.
-    Never claim "hypothesis generated/persisted" unless \`status_json.knowledge_state_summary.hypothesis_gate.accepted > 0\`
-    and \`status_json.recent_hypotheses\` is non-empty.
-
-Execution truth:
-  - Do not claim background progress unless you created a real async handle (job_id/task_id).
-  - Without a real async handle, execute synchronously in this turn and return status.
-  - If not executed, say not executed. Never imply hidden progress.
-
-Run profile defaults:
-  - Default profile: strict (full-text-first).
-  - Switch to fast/metadata-only only when user explicitly asks to skip full-text reading.
-  - Soft gate is default: non-fatal quality issues are warnings, not blockers.
-  - Never skip persistence due quality limits; persist every run.
-  - User-facing responses should be concise Markdown. Keep tool-call JSON minimal and only for persistence.
-  - Use degraded_quality only for fatal gate conditions.
-
-Research quality and gating:
-  - Full-text-first for core evidence papers.
-  - If full text unavailable: set full_text_read=false and unread_reason.
-  - Adaptive retrieval intent:
-    * early cycles: prioritize foundational/survey papers to establish field map
-    * later cycles: expand into mainstream variants and adjacent tracks
-    * when a hypothesis appears: immediately run one validation follow-up (supporting + critical evidence), do not wait for next heartbeat
-  - In core paper notes, avoid placeholders ("N/A", "not provided", "unknown"); either provide concrete content or omit field.
-  - Evidence binding for key conclusions should include section + locator + quote.
-  - BRIDGE requires resolvable evidence_ids and at least one full-text-backed evidence source.
-  - If BRIDGE, NEW+REVISE, or unread core backlog appears, execute one reflection follow-up query and persist trace/result.
-  - If a cycle is empty, do not stop at "no papers":
-    * diagnose whether it is query/alias/recency mismatch vs scope saturation
-    * persist diagnosis and next-query/pivot hints in run_log notes
-    * keep topic continuity, but prepare adjacent sub-direction queries that serve current idea validation
-  - Hypotheses are accepted only when evidence_ids and dependency_path are sufficient; otherwise reject via hypothesis_gate reasons.
-  - Before user-facing wording, check latest status.hypothesis_gate.accepted:
-    * accepted == 0: factual report only; do not output speculative "next high-value routes"/"deep dive" guidance.
-    * accepted > 0: include hypothesis details in current message by default (stable path).
-    * only when runtime/channel clearly supports multi-send, split into two consecutive messages (alert then detailed hypothesis).
-  - If hard user constraints are not met (for example min core papers), do not report status=ok.
-
-Traceability:
-  - Reuse prepare-returned scope/topic in record/status. Never replace scope with project_id.
-  - On follow-up ("which papers?", "why this hypothesis?"), answer from persisted status/knowledge_state first.
-  - Only re-search when persistence lacks required facts, and state this explicitly.
-
-Rigor:
-  - Never fabricate citations, quotes, venues, or results.
-  - Say "I don't know" when uncertain.
-  - Use \`python3\` (not \`python\`) for shell commands in this environment.`;
-const CRON_CONTEXT_GUARD = `
-[Scientify Cron Context]
-This turn is already running inside a cron-triggered execution.
-Do not call scientify_cron_job (or create another cron job) from this run.
-Do not recursively schedule run_now from within cron.
-Use the existing execution handle and complete prepare -> record -> status directly.
-If workload is too heavy for this turn, prefer sessions_spawn task delegation (with task id) instead of nested cron.`;
-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;
-const FORCE_EN_RE = /output language:\s*english|please use english|use english|英文回复|请用英文/iu;
-const LANGUAGE_PROMPT_ZH = `[Language]
-You must reply in Simplified Chinese for all user-facing content.
-If you are about to respond in English, translate to Chinese and output only Chinese.
-`;
-const LANGUAGE_PROMPT_EN = `[Language]
-You must reply in English for all user-facing content unless quoting sources.
-`;
+Skills: match research tasks to <available_skills>; read SKILL.md before acting.
+Workspace: $W/projects/<topic>/. Check /research-status before writing. Active project in $W/projects/.active.
+  survey/ — search_terms.json, raw_results.json, filtered_papers.json, clusters.json, report.md (literature-survey)
+  papers/ — organized by cluster direction, each with paper_list.md + {arxiv_id}/ .tex sources (literature-survey)
+  notes/ — per-paper deep analysis paper_{id}.md (research-survey). survey_res.md = method comparison table.
+  ideas/ — gaps.md, idea_1..5.md, selected_idea.md, summary.md (idea-generation)
+  review/ — reading_plan.md, notes/{id}.md, comparison.md, taxonomy.md, draft.md, bibliography.bib (write-review-paper)
+  plan_res.md (research-plan) → project/ + ml_res.md (research-implement) → iterations/judge_v*.md (research-review) → experiment_res.md (research-experiment)
+Scheduling: if user asks for recurring or delayed push delivery (e.g. tomorrow at 08:00, daily digest), use research-subscription skill and call scientify_cron_job to create a real schedule.
+If it is a plain reminder (not research), set scientify_cron_job.message and do not default to the literature pipeline.
+For recurring research pushes, use scientify_literature_state to prepare dedupe context and record both pushed paper IDs and structured knowledge_state (changes, updates, hypotheses, run_log).
+Full-text-first policy: for papers used as core evidence, read full text when possible and mark full_text_read=true; if not fully read, you must explicitly mark full_text_read=false with unread_reason.
+Structured paper record policy: for each core paper, populate domain/subdomains/cross-domain links/research goal/approach/methodology design/key contributions/practical insights/must-understand points/limitations/evidence anchors.
+Use temporary local directory for full-text files (e.g. /tmp/scientify-fulltext/<run-id>) and delete it after record; write cleanup status to run_log.temp_cleanup_status.
+Quality targets for research runs: core full-text coverage >=80%; evidence-binding rate >=90% (key conclusions must bind to section+locator+quote); citation error rate <2%. If full text is missing, do not keep high-confidence conclusions.
+For research records, include project_id when available so state can persist under project knowledge_state/.
+When user gives preference feedback (e.g. "more like this", "skip this direction", "prefer arxiv"), quietly persist it via scientify_literature_state action=feedback when scope/topic are inferable.
+Preference memory is backend-only: use it to rerank future pushes, do not expose memory internals unless user explicitly asks.
+Do not stop at explanation when user explicitly asks to set a schedule.
+Rules: file exists = step done (skip). Outputs immutable unless user asks. project/ mutable during review loop.
+Execution: always use \`python3\` (not \`python\`) for shell commands in this environment.
+Rigor: read first, think second, answer third. Never fabricate references or results. Every claim needs a source. Say "I don't know" when uncertain. Read actual papers, not just abstracts. Ground ideas in real papers.`;
 /**
  * Injects on every prompt build (survives compaction).
  */
 export function createResearchModeHook() {
-    return (_event, context) => {
-        const sessionKey = typeof context.sessionKey === "string" ? context.sessionKey : "";
-        const inCronContext = sessionKey.includes(":cron:");
-        const promptText = typeof _event.prompt === "string" ? _event.prompt : "";
-        let languagePrefix = "";
-        if (FORCE_EN_RE.test(promptText)) {
-            languagePrefix = LANGUAGE_PROMPT_EN;
-        }
-        else if (FORCE_ZH_RE.test(promptText)) {
-            languagePrefix = LANGUAGE_PROMPT_ZH;
-        }
-        const basePrompt = inCronContext ? `${RESEARCH_MODE_PROMPT}\n${CRON_CONTEXT_GUARD}` : RESEARCH_MODE_PROMPT;
-        return {
-            prependContext: languagePrefix ? `${languagePrefix}\n${basePrompt}` : basePrompt,
-        };
+    return (_event, _context) => {
+        return { prependContext: RESEARCH_MODE_PROMPT };
     };
 }
 //# sourceMappingURL=research-mode.js.map

package/dist/src/hooks/research-mode.js.map

@@ -1 +1 @@
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package/dist/src/hooks/scientify-signature.d.ts

@@ -1,4 +1,4 @@
-type BaseHookContext = {
+type BaseHookContext = Record<string, unknown> & {
     sessionKey?: string;
     agentId?: string;
 };

package/dist/src/hooks/scientify-signature.d.ts.map

@@ -1 +1 @@
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package/dist/src/hooks/scientify-signature.js

@@ -11,19 +11,16 @@ const SCIENTIFY_TOOLS = new Set([
 const SCIENTIFY_SKILLS = new Set([
     "idea-generation",
     "research-pipeline",
-    "research-collect",
     "research-survey",
     "research-plan",
     "research-implement",
     "research-review",
     "research-experiment",
+    "literature-survey",
     "write-review-paper",
     "research-subscription",
-    // Compatibility skills kept for migration windows.
-    "metabolism",
-    "metabolism-init",
 ]);
-const SCIENTIFY_SKILL_COMMAND_RE = /(?:^|\s)\/(idea-generation|research-pipeline|research-collect|research-survey|research-plan|research-implement|research-review|research-experiment|write-review-paper|research-subscription|research-subscribe|research-subscriptions|research-unsubscribe|metabolism|metabolism-init|metabolism-status)(?:\s|$)/i;
+const SCIENTIFY_SKILL_COMMAND_RE = /(?:^|\s)\/(idea-generation|research-pipeline|research-survey|research-plan|research-implement|research-review|research-experiment|literature-survey|write-review-paper|research-subscription)(?:\s|$)/i;
 const SIGNATURE_PROMPT = `[Scientify Signature]
 If this response is based on Scientify workflow execution (Scientify skills/tools), append this exact footer at the end of your reply:
 ---

package/dist/src/hooks/scientify-signature.js.map

@@ -1 +1 @@
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+{"version":3,"file":"scientify-signature.js","sourceRoot":"","sources":["../../../src/hooks/scientify-signature.ts"],"names":[],"mappings":"AAmBA,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC;IAC9B,cAAc;IACd,gBAAgB;IAChB,eAAe;IACf,eAAe;IACf,iBAAiB;IACjB,oBAAoB;IACpB,oBAAoB;IACpB,4BAA4B;CAC7B,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,iBAAiB;IACjB,mBAAmB;IACnB,iBAAiB;IACjB,eAAe;IACf,oBAAoB;IACpB,iBAAiB;IACjB,qBAAqB;IACrB,mBAAmB;IACnB,oBAAoB;IACpB,uBAAuB;CACxB,CAAC,CAAC;AAEH,MAAM,0BAA0B,GAC9B,wMAAwM,CAAC;AAE3M,MAAM,gBAAgB,GAAG;;;;sCAIa,CAAC;AAEvC,iEAAiE;AACjE,MAAM,uBAAuB,GAAG,IAAI,GAAG,EAAU,CAAC;AAElD,SAAS,cAAc,CAAC,KAAc,EAAE,OAAwB;IAC9D,IAAI,OAAO,CAAC,UAAU;QAAE,OAAO,OAAO,CAAC,UAAU,CAAC;IAClD,IAAI,OAAO,CAAC,OAAO;QAAE,OAAO,OAAO,CAAC,OAAO,CAAC;IAC5C,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QACvC,MAAM,MAAM,GAAG,KAAgC,CAAC;QAChD,IAAI,OAAO,MAAM,CAAC,UAAU,KAAK,QAAQ;YAAE,OAAO,MAAM,CAAC,UAAU,CAAC;QACpE,IAAI,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ;YAAE,OAAO,MAAM,CAAC,OAAO,CAAC;IAChE,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,iBAAiB,CAAC,IAAa;IACtC,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO,SAAS,CAAC;IAC/C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC;IAC7C,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC;AACpB,CAAC;AAED,SAAS,WAAW,CAAC,KAAc;IACjC,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC;IAC5C,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO,KAAK;aACT,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;aAChC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC;aACjC,IAAI,CAAC,IAAI,CAAC,CAAC;IAChB,CAAC;IACD,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QACvC,MAAM,MAAM,GAAG,KAAgC,CAAC;QAChD,IAAI,OAAO,MAAM,CAAC,IAAI,KAAK,QAAQ;YAAE,OAAO,MAAM,CAAC,IAAI,CAAC;QACxD,IAAI,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ;YAAE,OAAO,MAAM,CAAC,OAAO,CAAC;IAChE,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC;AAED,SAAS,0BAA0B,CAAC,QAAmB;IACrD,KAAK,IAAI,CAAC,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9C,MAAM,IAAI,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;QACzB,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;YAAE,SAAS;QAChD,MAAM,MAAM,GAAG,IAA+B,CAAC;QAC/C,MAAM,IAAI,GAAG,OAAO,MAAM,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9E,IAAI,IAAI,KAAK,MAAM;YAAE,SAAS;QAC9B,OAAO,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;IACrC,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC;AAED,SAAS,8BAA8B,CAAC,KAA0B,EAAE,WAAmB;IACrF,IAAI,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC;QACxC,uBAAuB,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;QACzC,OAAO;IACT,CAAC;IAED,IAAI,KAAK,CAAC,QAAQ,KAAK,gBAAgB;QAAE,OAAO;IAChD,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IACpD,IAAI,KAAK,IAAI,gBAAgB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;QACzC,uBAAuB,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;IAC3C,CAAC;AACH,CAAC;AAED,MAAM,UAAU,+BAA+B;IAC7C,OAAO,CAAC,KAA0B,EAAE,OAAwB,EAAQ,EAAE;QACpE,MAAM,WAAW,GAAG,cAAc,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;QACnD,IAAI,CAAC,WAAW;YAAE,OAAO;QACzB,8BAA8B,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;IACrD,CAAC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,iCAAiC;IAC/C,OAAO,CAAC,KAAc,EAAE,OAAwB,EAAQ,EAAE;QACxD,MAAM,WAAW,GAAG,cAAc,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;QACnD,IAAI,CAAC,WAAW;YAAE,OAAO;QAEzB,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;YAAE,OAAO;QAChD,MAAM,MAAM,GAAG,KAAgC,CAAC;QAChD,MAAM,IAAI,GAAG;YACX,WAAW,CAAC,MAAM,CAAC,IAAI,CAAC;YACxB,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC;YAC3B,WAAW,CAAC,MAAM,CAAC,WAAW,CAAC;YAC/B,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC;SAC5B;aACE,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC;aACjC,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,IAAI,0BAA0B,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YAC1C,uBAAuB,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;QAC3C,CAAC;IACH,CAAC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,kCAAkC;IAChD,OAAO,CAAC,KAA6B,EAAE,OAAwB,EAA2B,EAAE;QAC1F,MAAM,WAAW,GAAG,cAAc,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;QAEnD,IAAI,WAAW,IAAI,uBAAuB,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,CAAC;YAC5D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,CAAC;QAC9C,CAAC;QAED,yEAAyE;QACzE,MAAM,UAAU,GAAG,OAAO,KAAK,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;QACxE,MAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,0BAA0B,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QACrG,MAAM,QAAQ,GAAG,GAAG,UAAU,KAAK,YAAY,EAAE,CAAC;QAClD,IAAI,0BAA0B,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC9C,IAAI,WAAW,EAAE,CAAC;gBAChB,uBAAuB,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;YAC3C,CAAC;YACD,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,CAAC;QAC9C,CAAC;QAED,OAAO;IACT,CAAC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,+BAA+B;IAC7C,OAAO,CAAC,KAAc,EAAE,OAAwB,EAAQ,EAAE;QACxD,MAAM,WAAW,GAAG,cAAc,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC;QACnD,IAAI,CAAC,WAAW;YAAE,OAAO;QACzB,uBAAuB,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAC9C,CAAC,CAAC;AACJ,CAAC"}

package/dist/src/knowledge-state/render.d.ts

@@ -1,4 +1,4 @@
-import type { ExplorationTraceInput, HypothesisGateSummary, KnowledgeChangeInput, KnowledgeHypothesisInput, KnowledgePaperInput, KnowledgeUpdateInput, ReflectionTaskInput } from "./types.js";
+import type { ExplorationTraceInput, KnowledgeChangeInput, KnowledgeHypothesisInput, KnowledgePaperInput, KnowledgeUpdateInput } from "./types.js";
 export declare function dayKeyFromTimestamp(ts: number): string;
 export declare function slugifyTopic(raw: string): string;
 export declare function renderPaperNoteHeaderMarkdown(args: {
@@ -24,11 +24,6 @@ export declare function renderExplorationLogMarkdown(args: {
     trace: ExplorationTraceInput[];
     papers: KnowledgePaperInput[];
 }): string;
-export declare function renderReflectionLogMarkdown(args: {
-    now: string;
-    runId: string;
-    tasks: ReflectionTaskInput[];
-}): string;
 export declare function renderDailyChangesMarkdown(args: {
     now: string;
     runId: string;
@@ -49,7 +44,6 @@ export declare function renderHypothesisMarkdown(args: {
 export declare function renderKnowledgeIndexMarkdown(args: {
     now: string;
     topic: string;
-    runProfile: "fast" | "strict";
     topicFiles: string[];
     paperNotesCount: number;
     totalHypotheses: number;
@@ -64,8 +58,6 @@ export declare function renderKnowledgeIndexMarkdown(args: {
         reasons: string[];
     };
     unreadCorePaperIds: string[];
-    reflectionTasks: ReflectionTaskInput[];
-    hypothesisGate: HypothesisGateSummary;
     lastStatus?: string;
 }): string;
 //# sourceMappingURL=render.d.ts.map

package/dist/src/knowledge-state/render.d.ts.map

@@ -1 +1 @@
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package/dist/src/knowledge-state/render.js

@@ -1,28 +1,17 @@
-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;
 function normalizeText(raw) {
     return raw.trim().replace(/\s+/g, " ");
 }
-function cleanText(raw) {
-    if (typeof raw !== "string")
-        return undefined;
-    const normalized = normalizeText(raw);
-    if (!normalized)
-        return undefined;
-    if (PLACEHOLDER_TEXT_RE.test(normalized))
-        return undefined;
-    return normalized;
-}
 function toCsv(values) {
     if (!Array.isArray(values) || values.length === 0)
         return undefined;
-    const cleaned = values.map((item) => cleanText(item)).filter((item) => Boolean(item));
+    const cleaned = values.map((item) => item.trim()).filter((item) => item.length > 0);
     return cleaned.length > 0 ? cleaned.join(", ") : undefined;
 }
 function renderStringArray(lines, label, values) {
     if (!Array.isArray(values) || values.length === 0)
         return;
     for (const [idx, value] of values.entries()) {
-        const trimmed = cleanText(value);
+        const trimmed = value.trim();
         if (!trimmed)
             continue;
         lines.push(`   - ${label}_${idx + 1}: ${trimmed}`);
@@ -132,111 +121,60 @@ export function renderPaperNoteHeaderMarkdown(args) {
 }
 export function renderPaperNoteRunMarkdown(args) {
     const paper = args.paper;
-    const profileFieldChecks = [
-        { label: "domain", filled: Boolean(cleanText(paper.domain)) },
-        { label: "subdomains", filled: Boolean(toCsv(paper.subdomains)) },
-        { label: "cross_domain_links", filled: Boolean(toCsv(paper.crossDomainLinks)) },
-        { label: "research_goal", filled: Boolean(cleanText(paper.researchGoal)) },
-        { label: "approach", filled: Boolean(cleanText(paper.approach)) },
-        { label: "methodology_design", filled: Boolean(cleanText(paper.methodologyDesign)) },
-        { label: "key_contributions", filled: Boolean(paper.keyContributions && paper.keyContributions.length > 0) },
-        { label: "practical_insights", filled: Boolean(paper.practicalInsights && paper.practicalInsights.length > 0) },
-        {
-            label: "must_understand_points",
-            filled: Boolean(paper.mustUnderstandPoints && paper.mustUnderstandPoints.length > 0),
-        },
-        { label: "limitations", filled: Boolean(paper.limitations && paper.limitations.length > 0) },
-        { label: "evidence_anchors", filled: Boolean(paper.evidenceAnchors && paper.evidenceAnchors.length > 0) },
-    ];
-    const profileFilledCount = profileFieldChecks.filter((item) => item.filled).length;
-    const profileMissingFields = profileFieldChecks.filter((item) => !item.filled).map((item) => item.label);
     const lines = [
         `## Run ${args.runId}`,
         `- Time: ${args.now}`,
         `- Role in run: ${args.role}`,
-        `- Read status: ${cleanText(paper.readStatus) ?? (paper.fullTextRead ? "fulltext" : "metadata")}`,
+        `- Read status: ${paper.readStatus ?? (paper.fullTextRead ? "fulltext" : "metadata")}`,
         `- Full-text read: ${paper.fullTextRead === true ? "true" : "false"}`,
-        `- Profile coverage: ${profileFilledCount}/${profileFieldChecks.length}`,
     ];
-    if (profileMissingFields.length > 0)
-        lines.push(`- Missing fields: ${profileMissingFields.join(", ")}`);
-    if (cleanText(paper.fullTextSource))
-        lines.push(`- Full-text source: ${cleanText(paper.fullTextSource)}`);
-    if (cleanText(paper.fullTextRef))
-        lines.push(`- Full-text ref: ${cleanText(paper.fullTextRef)}`);
-    if (cleanText(paper.unreadReason))
-        lines.push(`- Unread reason: ${cleanText(paper.unreadReason)}`);
+    if (paper.fullTextSource?.trim())
+        lines.push(`- Full-text source: ${paper.fullTextSource.trim()}`);
+    if (paper.fullTextRef?.trim())
+        lines.push(`- Full-text ref: ${paper.fullTextRef.trim()}`);
+    if (paper.unreadReason?.trim())
+        lines.push(`- Unread reason: ${paper.unreadReason.trim()}`);
     lines.push("");
     lines.push("### Research Positioning");
-    const domain = cleanText(paper.domain);
-    const subdomains = toCsv(paper.subdomains);
-    const crossDomainLinks = toCsv(paper.crossDomainLinks);
-    if (domain)
-        lines.push(`- Domain: ${domain}`);
-    if (subdomains)
-        lines.push(`- Subdomains: ${subdomains}`);
-    if (crossDomainLinks)
-        lines.push(`- Cross-domain links: ${crossDomainLinks}`);
-    if (!domain && !subdomains && !crossDomainLinks) {
-        lines.push("- Pending enrichment: taxonomy fields were not extracted in this run.");
-    }
+    lines.push(`- Domain: ${paper.domain?.trim() || "N/A"}`);
+    lines.push(`- Subdomains: ${toCsv(paper.subdomains) ?? "N/A"}`);
+    lines.push(`- Cross-domain links: ${toCsv(paper.crossDomainLinks) ?? "N/A"}`);
     lines.push("");
     lines.push("### Study Focus");
-    const researchGoal = cleanText(paper.researchGoal);
-    const approach = cleanText(paper.approach);
-    const methodologyDesign = cleanText(paper.methodologyDesign);
-    if (researchGoal)
-        lines.push(`- Research goal: ${researchGoal}`);
-    if (approach)
-        lines.push(`- Approach: ${approach}`);
-    if (methodologyDesign)
-        lines.push(`- Methodology design: ${methodologyDesign}`);
-    if (!researchGoal && !approach && !methodologyDesign) {
-        lines.push("- Pending enrichment: study-focus fields were not extracted in this run.");
-    }
+    lines.push(`- Research goal: ${paper.researchGoal?.trim() || "N/A"}`);
+    lines.push(`- Approach: ${paper.approach?.trim() || "N/A"}`);
+    lines.push(`- Methodology design: ${paper.methodologyDesign?.trim() || "N/A"}`);
     lines.push("");
     lines.push("### Contributions");
-    const keyContributions = (paper.keyContributions ?? [])
-        .map((item) => cleanText(item))
-        .filter((item) => Boolean(item));
-    if (keyContributions.length > 0) {
-        lines.push(...keyContributions.map((item, idx) => `${idx + 1}. ${item}`));
+    if (paper.keyContributions && paper.keyContributions.length > 0) {
+        lines.push(...paper.keyContributions.map((item, idx) => `${idx + 1}. ${item}`));
     }
     else {
-        lines.push("- Pending enrichment: no concrete contribution extracted yet.");
+        lines.push("1. (not provided)");
     }
     lines.push("");
     lines.push("### Practical Insights");
-    const practicalInsights = (paper.practicalInsights ?? [])
-        .map((item) => cleanText(item))
-        .filter((item) => Boolean(item));
-    if (practicalInsights.length > 0) {
-        lines.push(...practicalInsights.map((item, idx) => `${idx + 1}. ${item}`));
+    if (paper.practicalInsights && paper.practicalInsights.length > 0) {
+        lines.push(...paper.practicalInsights.map((item, idx) => `${idx + 1}. ${item}`));
     }
     else {
-        lines.push("- Pending enrichment: no practical insight extracted yet.");
+        lines.push("1. (not provided)");
     }
     lines.push("");
     lines.push("### Must Understand");
-    const mustUnderstandPoints = (paper.mustUnderstandPoints ?? [])
-        .map((item) => cleanText(item))
-        .filter((item) => Boolean(item));
-    if (mustUnderstandPoints.length > 0) {
-        lines.push(...mustUnderstandPoints.map((item, idx) => `${idx + 1}. ${item}`));
+    if (paper.mustUnderstandPoints && paper.mustUnderstandPoints.length > 0) {
+        lines.push(...paper.mustUnderstandPoints.map((item, idx) => `${idx + 1}. ${item}`));
     }
     else {
-        lines.push("- Pending enrichment: key concepts to master were not extracted yet.");
+        lines.push("1. (not provided)");
     }
     lines.push("");
     lines.push("### Limitations");
-    const limitations = (paper.limitations ?? [])
-        .map((item) => cleanText(item))
-        .filter((item) => Boolean(item));
-    if (limitations.length > 0) {
-        lines.push(...limitations.map((item, idx) => `${idx + 1}. ${item}`));
+    if (paper.limitations && paper.limitations.length > 0) {
+        lines.push(...paper.limitations.map((item, idx) => `${idx + 1}. ${item}`));
     }
     else {
-        lines.push("- Pending enrichment: limitation analysis not extracted yet.");
+        lines.push("1. (not provided)");
     }
     lines.push("");
     lines.push("### Evidence Anchors");
@@ -251,12 +189,7 @@ export function renderPaperNoteRunMarkdown(args) {
         lines.push(...paper.keyEvidenceSpans.map((item, idx) => `${idx + 1}. ${item}`));
     }
     else {
-        if (paper.fullTextRead === true || paper.readStatus === "fulltext") {
-            lines.push("- Pending enrichment: add section + locator + quote evidence anchors.");
-        }
-        else {
-            lines.push("- Metadata-only read in this run; evidence anchors require full-text reading.");
-        }
+        lines.push("1. (not provided)");
     }
     lines.push("");
     return lines.join("\n");
@@ -306,29 +239,6 @@ export function renderExplorationLogMarkdown(args) {
     ];
     return lines.join("\n");
 }
-export function renderReflectionLogMarkdown(args) {
-    const lines = [
-        `## Run ${args.runId}`,
-        `- Time: ${args.now}`,
-        `- Reflection tasks: ${args.tasks.length}`,
-        "",
-        "### Tasks",
-        ...(args.tasks.length > 0
-            ? args.tasks.map((task, idx) => {
-                const attrs = [
-                    `trigger=${task.trigger}`,
-                    `priority=${task.priority}`,
-                    `status=${task.status}`,
-                    `query=${task.query}`,
-                    `reason=${task.reason}`,
-                ];
-                return `${idx + 1}. ${attrs.join(" | ")}`;
-            })
-            : ["- (none)"]),
-        "",
-    ];
-    return lines.join("\n");
-}
 export function renderDailyChangesMarkdown(args) {
     const groups = {
         NEW: [],
@@ -379,9 +289,9 @@ export function renderTopicUpdateMarkdown(args) {
     return lines.join("\n");
 }
 export function renderHypothesisMarkdown(args) {
-    const novelty = typeof args.hypothesis.novelty === "number" ? args.hypothesis.novelty : "pending";
-    const feasibility = typeof args.hypothesis.feasibility === "number" ? args.hypothesis.feasibility : "pending";
-    const impact = typeof args.hypothesis.impact === "number" ? args.hypothesis.impact : "pending";
+    const novelty = typeof args.hypothesis.novelty === "number" ? args.hypothesis.novelty : "N/A";
+    const feasibility = typeof args.hypothesis.feasibility === "number" ? args.hypothesis.feasibility : "N/A";
+    const impact = typeof args.hypothesis.impact === "number" ? args.hypothesis.impact : "N/A";
     const lines = [
         `# ${args.hypothesisId}`,
         "",
@@ -392,54 +302,10 @@ export function renderHypothesisMarkdown(args) {
         "## Statement",
         args.hypothesis.statement,
         "",
-        "## Problem Gap",
-        args.hypothesis.problemGap ?? "pending",
-        "",
-        "## Proposed Mechanism",
-        args.hypothesis.proposedMechanism ?? "pending",
-        "",
-        "## Novelty Rationale",
-        args.hypothesis.noveltyRationale ?? "pending",
-        "",
         "## Dependency Path",
         ...(args.hypothesis.dependencyPath && args.hypothesis.dependencyPath.length > 0
             ? args.hypothesis.dependencyPath.map((step, idx) => `${idx + 1}. ${step}`)
-            : ["- Pending enrichment: dependency path not extracted in this run."]),
-        "",
-        "## Falsifiable Predictions",
-        ...(args.hypothesis.falsifiablePredictions && args.hypothesis.falsifiablePredictions.length > 0
-            ? args.hypothesis.falsifiablePredictions.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Critical Assumptions",
-        ...(args.hypothesis.criticalAssumptions && args.hypothesis.criticalAssumptions.length > 0
-            ? args.hypothesis.criticalAssumptions.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Failure Modes",
-        ...(args.hypothesis.failureModes && args.hypothesis.failureModes.length > 0
-            ? args.hypothesis.failureModes.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Success Criteria",
-        ...(args.hypothesis.successCriteria && args.hypothesis.successCriteria.length > 0
-            ? args.hypothesis.successCriteria.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Strengths",
-        ...(args.hypothesis.strengths && args.hypothesis.strengths.length > 0
-            ? args.hypothesis.strengths.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Weaknesses",
-        ...(args.hypothesis.weaknesses && args.hypothesis.weaknesses.length > 0
-            ? args.hypothesis.weaknesses.map((item, idx) => `${idx + 1}. ${item}`)
-            : ["1. (none)"]),
-        "",
-        "## Research Plan",
-        ...(args.hypothesis.planSteps && args.hypothesis.planSteps.length > 0
-            ? args.hypothesis.planSteps.map((step, idx) => `${idx + 1}. ${step}`)
-            : ["1. (none)"]),
+            : ["1. (not provided)"]),
         "",
         "## Evidence IDs",
         ...(args.hypothesis.evidenceIds && args.hypothesis.evidenceIds.length > 0
@@ -448,7 +314,7 @@ export function renderHypothesisMarkdown(args) {
         "",
         "## Validation",
         `- Status: ${args.hypothesis.validationStatus ?? "unchecked"}`,
-        `- Notes: ${args.hypothesis.validationNotes ?? "pending"}`,
+        `- Notes: ${args.hypothesis.validationNotes ?? "N/A"}`,
         ...(args.hypothesis.validationEvidence && args.hypothesis.validationEvidence.length > 0
             ? [
                 "- Evidence:",
@@ -460,17 +326,6 @@ export function renderHypothesisMarkdown(args) {
         `- Novelty: ${novelty}`,
         `- Feasibility: ${feasibility}`,
         `- Impact: ${impact}`,
-        ...(args.hypothesis.strictEvaluation
-            ? [
-                `- Strict overall score: ${typeof args.hypothesis.strictEvaluation.overallScore === "number" ? args.hypothesis.strictEvaluation.overallScore : "pending"}`,
-                `- Strict decision: ${args.hypothesis.strictEvaluation.decision ?? "pending"}`,
-                `- Strict reason: ${args.hypothesis.strictEvaluation.reason ?? "pending"}`,
-            ]
-            : [
-                "- Strict overall score: pending",
-                "- Strict decision: pending",
-                "- Strict reason: pending",
-            ]),
         "",
     ];
     return lines.join("\n");
@@ -481,7 +336,6 @@ export function renderKnowledgeIndexMarkdown(args) {
         "",
         `- Updated: ${args.now}`,
         `- Topic: ${args.topic}`,
-        `- Run profile: ${args.runProfile}`,
         `- Topic files: ${args.topicFiles.length}`,
         `- Paper notes: ${args.paperNotesCount}`,
         `- Total hypotheses: ${args.totalHypotheses}`,
@@ -492,20 +346,12 @@ export function renderKnowledgeIndexMarkdown(args) {
         `- Full-text coverage: ${args.qualityGate.fullTextCoveragePct}%`,
         `- Evidence binding rate: ${args.qualityGate.evidenceBindingRatePct}%`,
         `- Citation error rate: ${args.qualityGate.citationErrorRatePct}%`,
-        `- Reflection tasks (executed): ${args.reflectionTasks.filter((task) => task.status === "executed").length}`,
-        `- Hypothesis gate: accepted=${args.hypothesisGate.accepted}, rejected=${args.hypothesisGate.rejected}`,
         "",
         "## Quality Notes",
         ...(args.qualityGate.reasons.length > 0 ? args.qualityGate.reasons.map((reason) => `- ${reason}`) : ["- (none)"]),
         ...(args.unreadCorePaperIds.length > 0
             ? ["- unread_core_paper_ids: " + args.unreadCorePaperIds.join(", ")]
             : ["- unread_core_paper_ids: (none)"]),
-        ...(args.hypothesisGate.rejectionReasons.length > 0
-            ? args.hypothesisGate.rejectionReasons.map((reason) => `- hypothesis_gate_reason: ${reason}`)
-            : ["- hypothesis_gate_reason: (none)"]),
-        ...(args.reflectionTasks.length > 0
-            ? ["- reflection_tasks: " + args.reflectionTasks.map((task) => `${task.trigger}:${task.status}`).join(", ")]
-            : ["- reflection_tasks: (none)"]),
         "",
         "## Topics",
         ...(args.topicFiles.length > 0 ? args.topicFiles.map((file) => `- ${file}`) : ["- (none)"]),