scientify 1.13.5 → 2.0.0

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

@@ -1 +1 @@
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+{"version":3,"file":"scientify-signature.d.ts","sourceRoot":"","sources":["../../../src/hooks/scientify-signature.ts"],"names":[],"mappings":"AAAA,KAAK,eAAe,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;IAC/C,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,KAAK,mBAAmB,GAAG;IACzB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CAClC,CAAC;AAEF,KAAK,sBAAsB,GAAG;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,gBAAgB,GAAG;IACtB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB,CAAC;AAgGF,wBAAgB,+BAA+B,KACrC,OAAO,mBAAmB,EAAE,SAAS,eAAe,KAAG,IAAI,CAKpE;AAED,wBAAgB,iCAAiC,KACvC,OAAO,OAAO,EAAE,SAAS,eAAe,KAAG,IAAI,CAmBxD;AAED,wBAAgB,kCAAkC,KACxC,OAAO,sBAAsB,EAAE,SAAS,eAAe,KAAG,gBAAgB,GAAG,IAAI,CAoB1F;AAED,wBAAgB,+BAA+B,KACrC,OAAO,OAAO,EAAE,SAAS,eAAe,KAAG,IAAI,CAKxD"}

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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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

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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 = [
         `# ${args.hypothesisId}`,
         "",
@@ -395,22 +305,7 @@ export function renderHypothesisMarkdown(args) {
         "## Dependency Path",
         ...(args.hypothesis.dependencyPath && args.hypothesis.dependencyPath.length > 0
             ? args.hypothesis.dependencyPath.map((step, idx) => `${idx + 1}. ${step}`)
-            : ["- Pending enrichment: dependency path not extracted in this run."]),
-        "",
-        "## Strengths",
-        ...(args.hypothesis.strengths && args.hypothesis.strengths.length > 0
-            ? args.hypothesis.strengths.map((item, idx) => `${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
@@ -419,7 +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:",
@@ -431,17 +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");
@@ -452,7 +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}`,
@@ -463,20 +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)"]),

package/dist/src/knowledge-state/render.js.map

@@ -1 +1 @@
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package/dist/src/knowledge-state/store.d.ts.map

@@ -1 +1 @@
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