scientify 1.13.6 → 2.1.0

package/dist/src/research-subscriptions/prompt.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"prompt.d.ts","sourceRoot":"","sources":["../../../src/research-subscriptions/prompt.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,YAAY,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AAkHpE,wBAAgB,yBAAyB,CACvC,OAAO,EAAE,IAAI,CACX,mBAAmB,EACjB,OAAO,GACP,SAAS,GACT,WAAW,GACX,WAAW,GACX,aAAa,GACb,SAAS,GACT,eAAe,GACf,cAAc,GACd,cAAc,GACd,UAAU,CACb,EACD,YAAY,EAAE,YAAY,CAAC,MAAM,CAAC,EAClC,QAAQ,EAAE,MAAM,EAChB,YAAY,CAAC,EAAE,IAAI,GAAG,IAAI,GACzB,MAAM,CAmRR;AAED,wBAAgB,WAAW,IAAI,MAAM,CAwBpC;AAED,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAElD"}
+{"version":3,"file":"prompt.d.ts","sourceRoot":"","sources":["../../../src/research-subscriptions/prompt.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,YAAY,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AA0DpE,wBAAgB,yBAAyB,CACvC,OAAO,EAAE,IAAI,CACX,mBAAmB,EACnB,OAAO,GAAG,SAAS,GAAG,WAAW,GAAG,WAAW,GAAG,aAAa,GAAG,SAAS,GAAG,eAAe,GAAG,cAAc,CAC/G,EACD,YAAY,EAAE,YAAY,CAAC,MAAM,CAAC,EAClC,QAAQ,EAAE,MAAM,GACf,MAAM,CAiRR;AAED,wBAAgB,WAAW,IAAI,MAAM,CAsBpC;AAED,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAElD"}

package/dist/src/research-subscriptions/prompt.js

@@ -1,9 +1,6 @@
 import { DEFAULT_SCORE_WEIGHTS, REMINDER_HINT_RE, RESEARCH_HINT_RE, SCIENTIFY_SIGNATURE_FOOTER, } from "./constants.js";
 import { formatScoreWeights, resolveCandidatePool } from "./parse.js";
 const RESEARCH_WORKFLOW_VERB_RE = /\b(search|survey|analy[sz]e|filter|track|monitor|update|summari[sz]e|report|plan)\b|检索|调研|筛选|跟踪|追踪|更新|总结|汇报|规划/u;
-const FULLTEXT_OPT_OUT_RE = /\b(metadata[-\s]?only|abstract[-\s]?only|no\s+full[-\s]?text|without\s+full[-\s]?text|quick\s+scan)\b|不需要全文|不用全文|只看摘要|仅摘要|只要元数据|不读全文/u;
-const TOPIC_NOISE_TOKEN_RE = /\b(?:smoke|test|testing|debug|dry[-\s]?run|trial|sandbox|e2e|staging)[-_ ]?\d{0,12}\b/giu;
-const DATE_NOISE_RE = /\b20\d{2}(?:[-_.]?\d{2})?(?:[-_.]?\d{2})?\b/g;
 function normalizeReminderText(raw) {
     let text = raw.trim();
     text = text.replace(/^(please\s+)?remind\s+(me|us|you)\s+(to\s+)?/i, "");
@@ -45,54 +42,6 @@ function deriveResearchTopicFromMessage(message) {
     const normalized = text.trim();
     return normalized.length > 0 ? normalized : message.trim();
 }
-function normalizeRetrievalTopic(topic) {
-    const stripped = topic.replace(TOPIC_NOISE_TOKEN_RE, " ").replace(DATE_NOISE_RE, " ").replace(/\s+/g, " ").trim();
-    return stripped.length > 0 ? stripped : topic.trim();
-}
-function inferPreferredLanguage(text) {
-    const trimmed = text.trim();
-    if (!trimmed)
-        return undefined;
-    if (/[\p{Script=Han}]/u.test(trimmed))
-        return "zh";
-    return undefined;
-}
-function formatLanguageDirective(lang) {
-    if (lang === "zh") {
-        return [
-            "0) Your Output language: Chinese (Simplified).",
-            "   - Use Chinese for all content, even if the prompt is in English.",
-        ];
-    }
-    return [];
-}
-function buildVariantKeywords(topic) {
-    const keywords = new Set();
-    const normalized = normalizeRetrievalTopic(topic);
-    const tokens = normalized
-        .toLowerCase()
-        .match(/[\p{L}\p{N}][\p{L}\p{N}_-]{1,47}/gu)
-        ?.map((item) => item.trim())
-        .filter((item) => item.length >= 3) ?? [];
-    if (normalized.length > 0)
-        keywords.add(normalized);
-    if (tokens.length >= 2) {
-        keywords.add(tokens.slice(0, 4).join(" "));
-        keywords.add(tokens.slice(0, 3).join("-"));
-    }
-    for (const token of tokens.slice(0, 8)) {
-        keywords.add(token);
-    }
-    return [...keywords].slice(0, 10);
-}
-function resolveRunProfile(options, effectiveTopic) {
-    if (options.metadataOnly === true)
-        return "fast";
-    const text = `${options.topic ?? ""} ${options.message ?? ""} ${effectiveTopic}`.trim();
-    if (text.length > 0 && FULLTEXT_OPT_OUT_RE.test(text))
-        return "fast";
-    return "strict";
-}
 function buildPreferencePayload(options) {
     const maxPapers = options.maxPapers ?? 5;
     const normalizedSources = options.sources?.map((item) => item.trim().toLowerCase()).filter(Boolean);
@@ -102,18 +51,14 @@ function buildPreferencePayload(options) {
         ...(normalizedSources && normalizedSources.length > 0 ? { sources: [...new Set(normalizedSources)] } : {}),
     };
 }
-export function buildScheduledTaskMessage(options, scheduleKind, scopeKey, languageHint) {
+export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
     const customMessage = options.message?.trim();
     const promotedTopic = !options.topic && customMessage && shouldPromoteMessageToResearchTopic(customMessage)
         ? deriveResearchTopicFromMessage(customMessage)
         : undefined;
-    const inferredLanguage = languageHint ??
-        inferPreferredLanguage(`${options.topic ?? ""} ${options.message ?? ""}`.trim());
-    const languageDirective = formatLanguageDirective(inferredLanguage);
     if (customMessage && !promotedTopic) {
         return [
             "Scheduled reminder task.",
-            ...languageDirective,
             `Please send this reminder now: \"${customMessage}\"`,
             "Keep the reminder concise and do not run a research workflow unless explicitly requested.",
         ].join("\n");
@@ -122,22 +67,15 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey, langu
     if (reminderFromTopic) {
         return [
             "Scheduled reminder task.",
-            ...languageDirective,
             `Please send this reminder now: \"${reminderFromTopic}\"`,
             "Keep the reminder concise and do not run a research workflow unless explicitly requested.",
         ].join("\n");
     }
     const trimmedTopic = (options.topic ?? promotedTopic)?.trim();
     const effectiveTopic = trimmedTopic || "active project research updates";
-    const retrievalTopic = normalizeRetrievalTopic(effectiveTopic);
-    const variantKeywords = buildVariantKeywords(retrievalTopic);
     const preferences = buildPreferencePayload(options);
-    const runProfile = resolveRunProfile(options, effectiveTopic);
     const projectId = options.projectId?.trim();
-    const candidatePoolBase = resolveCandidatePool(options.candidatePool, preferences.max_papers);
-    const candidatePool = runProfile === "strict"
-        ? Math.max(candidatePoolBase, Math.min(40, Math.max(24, preferences.max_papers * 4)))
-        : candidatePoolBase;
+    const candidatePool = resolveCandidatePool(options.candidatePool, preferences.max_papers);
     const scoreWeights = options.scoreWeights ?? DEFAULT_SCORE_WEIGHTS;
     const scoreWeightsText = formatScoreWeights(scoreWeights);
     const preparePayload = JSON.stringify({
@@ -147,222 +85,237 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey, langu
         ...(projectId ? { project_id: projectId } : {}),
         preferences,
     });
-    const strictRunLogTemplate = runProfile === "strict"
-        ? {
-            required_core_papers: Math.max(1, Math.min(preferences.max_papers, 3)),
-            required_full_text_coverage_pct: 80,
-        }
-        : {};
+    const recordPaperTemplate = [
+        {
+            id: "arxiv:2501.12345",
+            title: "Paper title",
+            url: "https://arxiv.org/abs/2501.12345",
+            score: 92,
+            reason: "High topical relevance and strong authority.",
+        },
+        {
+            id: "doi:10.1000/xyz123",
+            title: "Paper title 2",
+            url: "https://doi.org/10.1000/xyz123",
+            score: 88,
+            reason: "Novel method with clear practical impact.",
+        },
+    ];
+    const knowledgeStateTemplate = {
+        core_papers: [
+            {
+                id: "arxiv:2501.12345",
+                title: "Paper title",
+                url: "https://arxiv.org/abs/2501.12345",
+                source: "arxiv",
+                score: 92,
+                reason: "High topical relevance and strong authority.",
+                summary: "One-line core takeaway.",
+                evidence_ids: ["arxiv:2501.12345"],
+                full_text_read: true,
+                read_status: "fulltext",
+                full_text_source: "arxiv_pdf",
+                full_text_ref: "https://arxiv.org/pdf/2501.12345.pdf",
+                domain: "machine learning",
+                subdomains: ["parameter-efficient fine-tuning", "large language models"],
+                cross_domain_links: ["systems optimization"],
+                research_goal: "Improve adaptation quality while keeping trainable parameters very small.",
+                approach: "Introduce low-rank adapters and train only adapter matrices.",
+                methodology_design: "Compare with full fine-tuning across multiple model scales/tasks.",
+                key_contributions: ["Low-rank adaptation module design", "Parameter/memory efficiency evidence"],
+                practical_insights: ["Rank choice strongly affects stability and quality tradeoff"],
+                must_understand_points: ["Why low-rank decomposition works in adaptation layers"],
+                limitations: ["Task-specific rank sensitivity"],
+                key_evidence_spans: ["Eq.(3) shows ...", "Section 4 reports ..."],
+                evidence_anchors: [
+                    {
+                        section: "Method",
+                        locator: "Eq.(3)",
+                        claim: "Low-rank decomposition reduces trainable parameters drastically.",
+                        quote: "W = W0 + BA where rank(B,A) << d",
+                    },
+                ],
+            },
+        ],
+        exploration_papers: [
+            {
+                id: "doi:10.1000/xyz123",
+                title: "Paper title 2",
+                url: "https://doi.org/10.1000/xyz123",
+                source: "openalex",
+                score: 88,
+                reason: "Novel method with clear practical impact.",
+                full_text_read: false,
+                read_status: "metadata",
+                unread_reason: "Full text not accessible in this run.",
+            },
+        ],
+        exploration_trace: [
+            {
+                query: "P2D battery model physics-informed agent",
+                source: "arxiv",
+                candidates: 20,
+                filtered_to: 3,
+                filtered_out_reasons: ["off-topic", "weak authority"],
+                result_count: 3,
+            },
+        ],
+        knowledge_changes: [
+            {
+                type: "NEW",
+                statement: "New method/insight discovered in this run.",
+                evidence_ids: ["arxiv:2501.12345"],
+                topic: "example-topic",
+            },
+        ],
+        knowledge_updates: [
+            {
+                topic: "example-topic",
+                op: "append",
+                content: "Update knowledge base with this run's key finding.",
+                confidence: "medium",
+                evidence_ids: ["arxiv:2501.12345"],
+            },
+        ],
+        hypotheses: [
+            {
+                statement: "Potential hypothesis triggered by current changes.",
+                trigger: "TREND",
+                dependency_path: ["Prior unresolved question", "New supporting evidence"],
+                novelty: 3.5,
+                feasibility: 3.2,
+                impact: 4.1,
+                evidence_ids: ["arxiv:2501.12345"],
+                validation_status: "unchecked",
+                validation_notes: "Optional: run openreview_lookup or additional search before promotion.",
+                validation_evidence: [],
+            },
+        ],
+        run_log: {
+            model: "model-name",
+            duration_ms: 1200,
+            temp_full_text_dir: "/tmp/scientify-fulltext/run-123",
+            temp_files_downloaded: 3,
+            temp_cleanup_status: "done",
+            full_text_attempted: 3,
+            full_text_completed: 2,
+            notes: "short run note",
+        },
+    };
     const recordTemplate = JSON.stringify({
         action: "record",
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
-        run_profile: runProfile,
-        run_id: "run-<unique-id>",
         status: "ok",
-        papers: [{ id: "arxiv:2501.12345", title: "Paper title", url: "https://arxiv.org/abs/2501.12345" }],
-        knowledge_state: {
-            core_papers: [
-                {
-                    id: "arxiv:2501.12345",
-                    title: "Paper title",
-                    url: "https://arxiv.org/abs/2501.12345",
-                    full_text_read: true,
-                    domain: "machine learning",
-                    subdomains: ["parameter-efficient fine-tuning"],
-                    research_goal: "one-sentence goal",
-                    approach: "one-sentence approach",
-                    methodology_design: "one-sentence method setup",
-                    key_contributions: ["contribution 1", "contribution 2"],
-                    practical_insights: ["insight 1"],
-                    must_understand_points: ["must-understand 1"],
-                    limitations: ["limitation 1"],
-                    evidence_anchors: [
-                        {
-                            section: "Method",
-                            locator: "Eq.(3)",
-                            claim: "key claim",
-                            quote: "short quote from paper",
-                        },
-                    ],
-                },
-            ],
-            knowledge_changes: [{ type: "NEW", statement: "one concrete change", evidence_ids: ["arxiv:2501.12345"] }],
-            hypotheses: [
-                {
-                    statement: "one grounded hypothesis",
-                    trigger: "TREND",
-                    problem_gap: "what current literature still fails to solve",
-                    proposed_mechanism: "how and why the proposed method could solve the gap",
-                    novelty_rationale: "what is new versus closest prior methods",
-                    dependency_path: ["step 1 grounded in prior result", "step 2 links new evidence"],
-                    falsifiable_predictions: [
-                        "prediction 1 with measurable direction",
-                        "prediction 2 that should fail if mechanism is wrong",
-                    ],
-                    critical_assumptions: ["assumption 1", "assumption 2"],
-                    failure_modes: ["failure mode 1"],
-                    success_criteria: ["criterion 1 with threshold", "criterion 2 from ablation"],
-                    strengths: ["strong empirical signal", "clear implementation path"],
-                    weaknesses: ["limited external validity", "potential data bias"],
-                    plan_steps: [
-                        "Build a reproducible baseline pipeline first (for ML tasks, include a simple baseline such as random forest if applicable).",
-                        "Implement the proposed method and run controlled comparison.",
-                        "Run ablation and failure-case analysis, then decide accept/revise/reject.",
-                    ],
-                    strict_evaluation: {
-                        overall_score: 78,
-                        decision: "accept",
-                        reason: "Evidence and execution plan are sufficient for immediate validation.",
-                    },
-                    novelty: 4,
-                    feasibility: 4,
-                    impact: 4,
-                    evidence_ids: ["arxiv:2501.12345", "arxiv:2501.54321"],
-                },
-            ],
-            run_log: { run_profile: runProfile, notes: "short run note", ...strictRunLogTemplate },
-        },
+        papers: recordPaperTemplate,
+        knowledge_state: knowledgeStateTemplate,
     });
-    const recordDegradedTemplate = JSON.stringify({
+    const recordFallbackTemplate = JSON.stringify({
         action: "record",
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
-        run_profile: runProfile,
-        run_id: "run-<unique-id>-degraded",
-        status: "degraded_quality",
-        papers: [{ id: "arxiv:2501.12345", title: "Paper title", url: "https://arxiv.org/abs/2501.12345" }],
+        status: "fallback_representative",
+        papers: recordPaperTemplate,
         knowledge_state: {
-            run_log: { run_profile: runProfile, degraded: true, notes: "quality not fully met in this run", ...strictRunLogTemplate },
+            ...knowledgeStateTemplate,
+            run_log: {
+                model: "model-name",
+                duration_ms: 1300,
+                degraded: true,
+                temp_full_text_dir: "/tmp/scientify-fulltext/run-123",
+                temp_files_downloaded: 1,
+                temp_cleanup_status: "done",
+                full_text_attempted: 1,
+                full_text_completed: 0,
+                notes: "Fallback pass was used because incremental pass had no unseen papers.",
+            },
         },
-        note: "selected papers persisted with degraded quality",
+        note: "No unseen papers this cycle; delivered best representative papers instead.",
     });
     const recordEmptyTemplate = JSON.stringify({
         action: "record",
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
-        run_profile: runProfile,
-        run_id: "run-20260309T103000Z-empty",
         status: "empty",
         papers: [],
         knowledge_state: {
+            core_papers: [],
+            exploration_papers: [],
+            exploration_trace: [],
+            knowledge_changes: [],
+            knowledge_updates: [],
+            hypotheses: [],
             run_log: {
-                run_profile: runProfile,
-                notes: "No suitable paper found in this cycle. empty_cycle_diagnosis=query_or_recency_mismatch_or_scope_saturation || empty_cycle_next_queries=<q1>|<q2>|<q3> || empty_cycle_pivot_hint=<how this serves current idea>",
-                ...strictRunLogTemplate,
+                model: "model-name",
+                temp_cleanup_status: "not_needed",
+                notes: "No suitable paper found in this cycle.",
             },
         },
         note: "No suitable paper found in incremental pass and fallback representative pass.",
     });
-    const variantHintLine = variantKeywords.length > 0 ? `- Expansion keywords: ${variantKeywords.join(", ")}` : "- Expansion keywords: (none)";
-    const languageDirectiveLines = languageDirective.length > 0 ? languageDirective : formatLanguageDirective(inferPreferredLanguage(effectiveTopic));
     if (scheduleKind === "at") {
         return [
             `/research-pipeline Run a focused literature study on \"${effectiveTopic}\" and return up to ${preferences.max_papers} high-value representative papers.`,
             "",
-            "Workflow (simple, Markdown-first):",
-            ...languageDirectiveLines,
-            "1) Complete 5 steps in this turn: retrieve -> filter -> read -> save metadata -> update knowledge/hypothesis.",
-            "2) First call prepare:",
-            `${preparePayload}`,
-            `3) Build candidate pool around ${candidatePool}; select up to ${preferences.max_papers} credible papers.`,
-            `   - Retrieval topic (normalized): ${retrievalTopic}`,
-            `   ${variantHintLine}`,
-            "   - Filter policy: semantic relevance, not exact string match; include important variants and aliases.",
-            "   - If user asks special constraints (foundational-first / avoid benchmark-only / prefer survey or authoritative papers), apply them in filtering and ranking.",
-            "   - If core candidates < 3, relax filters and rerun with broader query terms before declaring empty.",
-            `4) Reading policy: ${runProfile === "strict" ? "full-text required by default (strict)." : "metadata-only allowed (explicit opt-out detected)."}`,
-            "   - Never drop a relevant paper only because full text failed; keep it with full_text_read=false and unread_reason.",
-            "   - Early cycles should prioritize foundational/survey papers; later cycles should shift to mainstream variants and adjacent tracks.",
-            "5) User-facing answer MUST be concise Markdown:",
-            "   - Selected papers (numbered, title + URL + one-line value)",
-            "   - Read status (fulltext vs metadata)",
-            "   - For each selected paper: domain/subdomains + goal + approach + methodology + contributions + insights + limitations",
-            "   - Knowledge updates (NEW/CONFIRM/REVISE/BRIDGE)",
-            "   - Hypothesis decision (generated or not + reason)",
-            "   - If trigger signals are present (e.g. NEW>=2, or NEW+REVISE>=2, or BRIDGE present), propose 1 grounded hypothesis with >=2 evidence_ids and dependency_path>=2",
-            "   - Present hypothesis as a research card: gap, mechanism, novelty, falsifiable predictions, assumptions, failure modes, success criteria, executable plan.",
-            "   - Hypothesis must include: problem_gap, proposed_mechanism, novelty_rationale, falsifiable_predictions>=2, critical_assumptions>=2, failure_modes>=1, success_criteria>=2, strengths>=2, weaknesses>=2, plan_steps>=3, strict_evaluation (overall_score + decision + reason).",
-            "   - Plan must be executable; when task is predictive/modeling, include at least one lightweight baseline idea (e.g., random forest).",
-            "6) Persist once via `scientify_literature_state.record` using MINIMAL JSON only:",
-            `${recordTemplate}`,
-            "7) Soft-gate default: non-fatal quality gaps should keep status=`ok` and be reported as warnings in quality_gate.",
-            "8) Execute one immediate reflection follow-up when trigger signals exist (hypothesis generated, BRIDGE, NEW+REVISE, unread core), and write trace/results back into knowledge_state.",
-            "9) Use `degraded_quality` only for fatal gate issues (do not skip record):",
-            `${recordDegradedTemplate}`,
-            "10) Before using `empty`, perform empty-cycle diagnosis:",
-            "    - Check whether query/alias/recency is too narrow.",
-            "    - Check whether this sub-direction is likely saturated (few unseen papers across repeated cycles).",
-            "    - Propose 2-3 next queries and one pivot hint tied to current idea validation (supporting + critical evidence).",
-            "11) Use `empty` only when no paper is selected after both primary and broadened fallback retrieval:",
+            "Mandatory workflow:",
+            `1) Call tool \`scientify_literature_state\` with: ${preparePayload}`,
+            "2) Read `memory_hints` from prepare result. Treat preferred keywords/sources as positive ranking priors, and avoided ones as negative priors.",
+            `3) Build a candidate pool of around ${candidatePool} papers when possible, matching returned preferences (sources/recency).`,
+            `4) Score each candidate with weighted dimensions (${scoreWeightsText}). Each dimension is 0-100, then compute weighted average score.`,
+            `5) Apply memory prior adjustment to the score (up-rank preferred keyword/source matches; down-rank avoided matches).`,
+            `6) Select top ${preferences.max_papers} papers.`,
+            "7) Create a temporary local directory for full text (for example `/tmp/scientify-fulltext/<run-id>`). Download full text for selected core papers when possible (arXiv PDF/source first, then DOI OA PDF if available).",
+            "8) Read full text with `paper_browser` in sections (method, experiments, limitations). Extract structured fields per paper: `domain`, `subdomains`, `cross_domain_links`, `research_goal`, `approach`, `methodology_design`, `key_contributions`, `practical_insights`, `must_understand_points`, `limitations`, and `evidence_anchors`.",
+            "9) For papers without full text, explicitly set `full_text_read=false` and provide `unread_reason`.",
+            `10) Call \`scientify_literature_state\` to persist selected papers and knowledge_state details using this JSON shape: ${recordTemplate}`,
+            "11) `knowledge_state.core_papers` must include all selected papers with id/title/url/score/reason and structured reading fields (not placeholders).",
+            "12) `knowledge_state.knowledge_changes` and `knowledge_state.knowledge_updates` must reflect this run's actual findings and include `evidence_ids` whenever available.",
+            "13) Quality targets must be met: core full-text coverage >= 80%, evidence-binding rate >= 90% (key conclusions backed by section+locator+quote), citation error rate < 2%.",
+            "14) Without sufficient full-text evidence, do not keep high-confidence conclusions; downgrade confidence explicitly.",
+            "15) For hypotheses, include at least one `evidence_ids` entry and a concrete `dependency_path` when applicable. Prioritize evidence from full-text-read papers.",
+            "16) If a hypothesis is high-impact, optionally run `openreview_lookup` or additional literature search and fill `validation_status`/`validation_notes`/`validation_evidence`.",
+            "17) After recording state, clean temporary full-text files. Put cleanup outcome in `run_log.temp_cleanup_status` (`done|partial|failed|not_needed`) and optional `temp_cleanup_note`.",
+            "18) Keep `run_log.notes` factual (candidate count, filtering reason, fallback/no-fallback).",
+            "19) In user-facing output, always include a numbered paper list with title + direct source URL + one-line value. Never claim papers were selected without listing links.",
+            "20) Do not display raw score/reason unless explicitly requested.",
+            "21) If nothing suitable is found, still call record with empty papers using:",
             `${recordEmptyTemplate}`,
-            "12) After record, call status and include `run_id`/`latest_run_id`.",
-            "    - Use status as the single source of truth. Never claim hypothesis persisted unless status.hypothesis_gate.accepted > 0 and status.recent_hypotheses is non-empty.",
-            "13) Response policy based on hypothesis gate:",
-            "   - Read `status.knowledge_state_summary.hypothesis_gate.accepted` before final answer.",
-            "   - If accepted == 0: output factual cycle report only (papers/read-status/changes/gates). Do NOT output speculative roadmap/high-value-routes/deep-dive suggestions.",
-            "   - If accepted > 0: include hypothesis details in the current message by default (stable delivery path).",
-            "   - If runtime/channel clearly supports multi-send, you may split into two consecutive messages:",
-            "     Message 1: short alert (topic + accepted hypothesis count + cycle status).",
-            "     Message 2: hypothesis details (statement, evidence_ids, dependency_path, strict evaluation, executable next steps).",
-            "Never write placeholders like 'not provided'/'N/A' in core_papers fields. If unavailable, omit the field or set unread_reason.",
-            "Do not output large JSON to users; JSON is for tool call only.",
+            "Then respond: `No new literature found.`",
         ].join("\n");
     }
     return [
         `/research-pipeline Run an incremental literature check focused on \"${effectiveTopic}\".`,
         "",
-        "Workflow (simple, Markdown-first):",
-        ...languageDirectiveLines,
-        "1) Complete 5 steps in this turn: retrieve -> filter -> read -> save metadata -> update knowledge/hypothesis.",
-        "2) First call prepare:",
-        `${preparePayload}`,
-        `3) Build candidate pool around ${candidatePool}; select up to ${preferences.max_papers} credible unseen papers.`,
-        `4) Rank with weights (${scoreWeightsText}), while respecting memory hints and dedupe.`,
-        `   - Retrieval topic (normalized): ${retrievalTopic}`,
-        `   ${variantHintLine}`,
-        "   - Filter policy: semantic relevance, not exact string match; include major method variants.",
-        "   - If user asks special constraints (foundational-first / avoid benchmark-only / prefer survey or authoritative papers), apply them in filtering and ranking.",
-        "   - If selected core papers < 3, broaden query and rerun once before returning empty.",
-        `5) Reading policy: ${runProfile === "strict" ? "full-text required by default (strict)." : "metadata-only allowed (explicit opt-out detected)."}`,
-        "   - Never drop a relevant paper only because full text failed; keep it with full_text_read=false and unread_reason.",
-        "   - Early cycles should prioritize foundational/survey papers; later cycles should shift to mainstream variants and adjacent tracks.",
-        "6) User-facing answer MUST be concise Markdown:",
-        "   - Selected papers (numbered, title + URL + one-line value)",
-        "   - Read status (fulltext vs metadata)",
-        "   - For each selected paper: domain/subdomains + goal + approach + methodology + contributions + insights + limitations",
-        "   - Knowledge updates (NEW/CONFIRM/REVISE/BRIDGE)",
-        "   - Hypothesis decision (generated or not + reason)",
-        "   - If trigger signals are present (e.g. NEW>=2, or NEW+REVISE>=2, or BRIDGE present), propose 1 grounded hypothesis with >=2 evidence_ids and dependency_path>=2",
-        "   - Present hypothesis as a research card: gap, mechanism, novelty, falsifiable predictions, assumptions, failure modes, success criteria, executable plan.",
-        "   - Hypothesis must include: problem_gap, proposed_mechanism, novelty_rationale, falsifiable_predictions>=2, critical_assumptions>=2, failure_modes>=1, success_criteria>=2, strengths>=2, weaknesses>=2, plan_steps>=3, strict_evaluation (overall_score + decision + reason).",
-        "   - Plan must be executable; when task is predictive/modeling, include at least one lightweight baseline idea (e.g., random forest).",
-        "7) Persist once via `scientify_literature_state.record` using MINIMAL JSON only:",
-        `${recordTemplate}`,
-        "8) Soft-gate default: non-fatal quality gaps should keep status=`ok` and be reported as warnings in quality_gate.",
-        "9) Execute one immediate reflection follow-up when trigger signals exist (hypothesis generated, BRIDGE, NEW+REVISE, unread core), and write trace/results back into knowledge_state.",
-        "10) Use `degraded_quality` only for fatal gate issues (do not skip record):",
-        `${recordDegradedTemplate}`,
-        "11) Before using `empty`, perform empty-cycle diagnosis:",
-        "    - Check whether query/alias/recency is too narrow.",
-        "    - Check whether this sub-direction is likely saturated (few unseen papers across repeated cycles).",
-        "    - Propose 2-3 next queries and one pivot hint tied to current idea validation (supporting + critical evidence).",
-        "12) If both incremental and broadened fallback passes are empty, persist empty:",
+        "Mandatory workflow:",
+        `1) Call tool \`scientify_literature_state\` with: ${preparePayload}`,
+        "2) Read `memory_hints` from prepare result. Use them as quiet personalization priors in ranking (not user-facing).",
+        "3) Treat `exclude_paper_ids` as hard dedupe constraints. Do not push papers whose IDs are already in that list.",
+        `4) Incremental pass: build a candidate pool of around ${candidatePool} unseen papers when possible, following preferences (sources/recency).`,
+        `5) Score each candidate with weighted dimensions (${scoreWeightsText}). Each dimension is 0-100, then compute weighted average score.`,
+        "6) Apply memory prior adjustment to the score (up-rank preferred keyword/source matches; down-rank avoided matches).",
+        `7) Select at most ${preferences.max_papers} top-ranked unseen papers.`,
+        "8) Create a temporary local directory for full text (for example `/tmp/scientify-fulltext/<run-id>`). Download full text for selected core papers when possible (arXiv first, then DOI OA if available).",
+        "9) Read full text with `paper_browser` and fill structured paper fields: `domain`, `subdomains`, `cross_domain_links`, `research_goal`, `approach`, `methodology_design`, `key_contributions`, `practical_insights`, `must_understand_points`, `limitations`, and `evidence_anchors`.",
+        "10) If full text cannot be read, set `full_text_read=false` with explicit `unread_reason`.",
+        `11) If selected > 0, call \`scientify_literature_state\` with status \`ok\` using: ${recordTemplate}`,
+        "12) `knowledge_state.core_papers` must contain all selected papers with id/title/url/score/reason and structured reading fields; `exploration_trace` should include query/source/candidates/filtered_to/filter reasons when available.",
+        "13) `knowledge_state.knowledge_changes` and `knowledge_state.hypotheses` should include evidence_ids (and dependency_path for hypotheses) whenever available, preferably from full-text-read papers.",
+        "14) Quality targets must be met: core full-text coverage >= 80%, evidence-binding rate >= 90% (key conclusions backed by section+locator+quote), citation error rate < 2%.",
+        "15) Without sufficient full-text evidence, do not keep high-confidence conclusions; downgrade confidence explicitly.",
+        "16) For top hypotheses, optionally validate risk via `openreview_lookup` and fill `validation_status`/`validation_notes`/`validation_evidence`.",
+        "17) If incremental selection is empty, run one fallback representative pass (ignore `exclude_paper_ids` once) and select best representative papers.",
+        `18) If fallback returns papers, call \`scientify_literature_state\` with status \`fallback_representative\` using: ${recordFallbackTemplate}`,
+        "19) After recording state, clean temporary full-text files and set `run_log.temp_cleanup_status` accordingly (`done|partial|failed|not_needed`).",
+        "20) If papers are selected (incremental or fallback), output a numbered list with title + direct source URL + one-line value for each pushed paper.",
+        "21) Output a compact progress report for this cycle: what changed, what matters, and a concrete plan for the next 1 hour.",
+        "22) If a hypothesis is generated, explain *why* it is reasonable based on what was read (e.g., which findings connect), but do NOT list trigger conditions or say 'triggered by BRIDGE/NEW'.",
+        "23) Keep user-facing output concise; do not expose raw score/reason unless explicitly requested.",
+        "24) If both incremental and fallback passes are empty, call record with empty papers using:",
         `${recordEmptyTemplate}`,
-        "13) After record, call status and include `run_id`/`latest_run_id` for traceability.",
-        "    - Use status as the single source of truth. Never claim hypothesis persisted unless status.hypothesis_gate.accepted > 0 and status.recent_hypotheses is non-empty.",
-        "14) Response policy based on hypothesis gate:",
-        "   - Read `status.knowledge_state_summary.hypothesis_gate.accepted` before final answer.",
-        "   - If accepted == 0: output factual cycle report only (papers/read-status/changes/gates). Do NOT output speculative roadmap/high-value-routes/deep-dive suggestions.",
-        "   - If accepted > 0: include hypothesis details in the current message by default (stable delivery path).",
-        "   - If runtime/channel clearly supports multi-send, you may split into two consecutive messages:",
-        "     Message 1: short alert (topic + accepted hypothesis count + cycle status).",
-        "     Message 2: hypothesis details (statement, evidence_ids, dependency_path, strict evaluation, executable next steps).",
-        "Never write placeholders like 'not provided'/'N/A' in core_papers fields. If unavailable, omit the field or set unread_reason.",
-        "Do not output large JSON to users; JSON is for tool call only.",
+        "25) Then still return a useful progress status with next-hour actions (instead of only a generic reminder).",
     ].join("\n");
 }
 export function formatUsage() {
@@ -384,8 +337,6 @@ export function formatUsage() {
         "- `/research-subscribe daily 08:00 --topic \"LLM alignment\"`",
         "- `/research-subscribe daily 08:00 --topic \"LLM alignment\" --max-papers 5 --sources arxiv,openalex`",
         "- `/research-subscribe daily 08:00 --topic \"LLM alignment\" --candidate-pool 12 --score-weights relevance:45,novelty:20,authority:25,actionability:10`",
-        "- `/research-subscribe daily 08:00 --topic \"LLM alignment\" --metadata-only`",
-        "- `/research-subscribe daily 09:00 --topic \"LLM alignment\" --language zh`",
         "- `/research-subscribe at 1m --message \"Time to drink coffee.\"`",
         "- `/research-subscribe daily 09:00 --no-deliver`",
     ].join("\n");

package/dist/src/research-subscriptions/prompt.js.map

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