scientify 1.12.0 → 1.12.1

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

@@ -194,6 +194,8 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
         run_log: {
             model: "model-name",
             duration_ms: 1200,
+            required_core_papers: preferences.max_papers,
+            required_full_text_coverage_pct: 80,
             temp_full_text_dir: "/tmp/scientify-fulltext/run-123",
             temp_files_downloaded: 3,
             temp_cleanup_status: "done",
@@ -207,6 +209,7 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
+        run_id: "run-20260309T103000Z",
         status: "ok",
         papers: recordPaperTemplate,
         knowledge_state: knowledgeStateTemplate,
@@ -216,6 +219,7 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
+        run_id: "run-20260309T103000Z-fallback",
         status: "fallback_representative",
         papers: recordPaperTemplate,
         knowledge_state: {
@@ -224,6 +228,8 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
                 model: "model-name",
                 duration_ms: 1300,
                 degraded: true,
+                required_core_papers: preferences.max_papers,
+                required_full_text_coverage_pct: 80,
                 temp_full_text_dir: "/tmp/scientify-fulltext/run-123",
                 temp_files_downloaded: 1,
                 temp_cleanup_status: "done",
@@ -239,6 +245,7 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
         scope: scopeKey,
         topic: effectiveTopic,
         ...(projectId ? { project_id: projectId } : {}),
+        run_id: "run-20260309T103000Z-empty",
         status: "empty",
         papers: [],
         knowledge_state: {
@@ -250,6 +257,8 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
             hypotheses: [],
             run_log: {
                 model: "model-name",
+                required_core_papers: preferences.max_papers,
+                required_full_text_coverage_pct: 80,
                 temp_cleanup_status: "not_needed",
                 notes: "No suitable paper found in this cycle.",
             },
@@ -261,7 +270,11 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
             `/research-pipeline Run a focused literature study on \"${effectiveTopic}\" and return up to ${preferences.max_papers} high-value representative papers.`,
             "",
             "Mandatory workflow:",
+            "0) Truthfulness contract: do not claim background progress unless a real async handle exists. If you did not create a cron job/task id, this run must finish in this turn.",
+            "0.1) This run already has an async handle (cron). Do not call `scientify_cron_job` again from inside this run, and do not create nested `run_now` jobs.",
             `1) Call tool \`scientify_literature_state\` with: ${preparePayload}`,
+            "1.1) `no_deliver` only controls delivery. You still must call `scientify_literature_state.record` for persistence.",
+            "1.2) Reuse the exact `scope` and `topic` returned by `prepare` in `record` and `status`. Do not replace scope with project id.",
             "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.`,
@@ -270,27 +283,36 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
             "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`.",
+            "9.1) Set a unique `run_id` for this cycle (cron run id preferred; otherwise generate a timestamp-based id). Reusing the same run_id can cause idempotent no-op writes.",
             `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:",
+            "15) If `knowledge_changes` contains BRIDGE (or REVISE+CONFIRM contradiction signals), run at least one reflection query immediately and write it into `knowledge_state.exploration_trace` with query/reason/source/candidates/filtered_to.",
+            "15.1) Do not emit BRIDGE without grounded evidence_ids linked to this run's papers; at least one bridge evidence should be full-text-backed.",
+            "16) For hypotheses, use research-grade gate: at least 2 `evidence_ids`, dependency_path length >= 2, and include novelty+feasibility+impact scores. Evidence should be resolved and preferably full-text-backed.",
+            "16.1) If user provided hard constraints (for example exact/min core paper count), set `run_log.required_core_papers` accordingly and do not return status `ok` unless the requirement is met.",
+            "17) If a hypothesis is high-impact, optionally run `openreview_lookup` or additional literature search and fill `validation_status`/`validation_notes`/`validation_evidence`.",
+            "18) 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`.",
+            "19) Keep `run_log.notes` factual (candidate count, filtering reason, reflection action, fallback/no-fallback).",
+            "20) 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.",
+            "21) Do not display raw score/reason unless explicitly requested.",
+            "22) If nothing suitable is found, still call record with empty papers using:",
             `${recordEmptyTemplate}`,
             "Then respond: `No new literature found.`",
+            "23) After `record`, call `scientify_literature_state.status` once and include `run_id`/`latest_run_id` in your response for verifiable traceability.",
         ].join("\n");
     }
     return [
         `/research-pipeline Run an incremental literature check focused on \"${effectiveTopic}\".`,
         "",
         "Mandatory workflow:",
+        "0) Truthfulness contract: do not claim background progress unless a real async handle exists. If you did not create a cron job/task id, this run must finish in this turn.",
+        "0.1) This run already has an async handle (cron). Do not call `scientify_cron_job` again from inside this run, and do not create nested `run_now` jobs.",
         `1) Call tool \`scientify_literature_state\` with: ${preparePayload}`,
+        "1.1) `no_deliver` only controls delivery. You still must call `scientify_literature_state.record` for persistence.",
+        "1.2) Reuse the exact `scope` and `topic` returned by `prepare` in `record` and `status`. Do not replace scope with project id.",
         "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).`,
@@ -300,21 +322,27 @@ export function buildScheduledTaskMessage(options, scheduleKind, scopeKey) {
         "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`.",
+        "10.1) Set a unique `run_id` for this cycle (cron run id preferred; otherwise generate a timestamp-based id). Reusing the same run_id can cause idempotent no-op writes.",
         `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) Keep user-facing output concise; do not expose raw score/reason unless explicitly requested.",
-        "23) If both incremental and fallback passes are empty, call record with empty papers using:",
+        "16) If `knowledge_changes` contains BRIDGE (or REVISE+CONFIRM contradiction signals), run at least one reflection query immediately and write it into `knowledge_state.exploration_trace` with query/reason/source/candidates/filtered_to.",
+        "16.1) Do not emit BRIDGE without grounded evidence_ids linked to this run's papers; at least one bridge evidence should be full-text-backed.",
+        "17) Research-grade hypothesis gate: each hypothesis should have >=2 evidence_ids, dependency_path length >=2, novelty+feasibility+impact scores, and evidence linked to this run's papers (full-text-backed when possible).",
+        "17.1) If user provided hard constraints (for example exact/min core paper count), set `run_log.required_core_papers` accordingly and do not return status `ok` unless the requirement is met.",
+        "18) For top hypotheses, optionally validate risk via `openreview_lookup` and fill `validation_status`/`validation_notes`/`validation_evidence`.",
+        "19) If incremental selection is empty, run one fallback representative pass (ignore `exclude_paper_ids` once) and select best representative papers.",
+        `20) If fallback returns papers, call \`scientify_literature_state\` with status \`fallback_representative\` using: ${recordFallbackTemplate}`,
+        "21) After recording state, clean temporary full-text files and set `run_log.temp_cleanup_status` accordingly (`done|partial|failed|not_needed`).",
+        "22) If papers are selected (incremental or fallback), output a numbered list with title + direct source URL + one-line value for each pushed paper.",
+        "23) Output a compact progress report for this cycle: what changed, what matters, and a concrete plan for the next 1 hour.",
+        "24) Keep user-facing output concise; do not expose raw score/reason unless explicitly requested.",
+        "25) If both incremental and fallback passes are empty, call record with empty papers using:",
         `${recordEmptyTemplate}`,
-        "24) Then still return a useful progress status with next-hour actions (instead of only a generic reminder).",
+        "26) Then still return a useful progress status with next-hour actions (instead of only a generic reminder).",
+        "27) After `record`, call `scientify_literature_state.status` and include `run_id`/`latest_run_id` in your response for verifiable traceability.",
     ].join("\n");
 }
 export function formatUsage() {

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

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package/dist/src/tools/scientify-cron.d.ts

@@ -19,6 +19,7 @@ export declare const ScientifyCronToolSchema: import("@sinclair/typebox").TObjec
     channel: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
     to: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
     no_deliver: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
+    run_now: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
     job_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
 }>;
 type CronToolDeps = {
@@ -49,6 +50,7 @@ export declare function createScientifyCronTool(deps: CronToolDeps): {
         channel: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
         to: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
         no_deliver: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
+        run_now: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
         job_id: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
     }>;
     execute: (_toolCallId: string, rawArgs: unknown) => Promise<{

package/dist/src/tools/scientify-cron.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scientify-cron.d.ts","sourceRoot":"","sources":["../../../src/tools/scientify-cron.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAA6C,YAAY,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AASvG,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;EAmFlC,CAAC;AAEH,KAAK,YAAY,GAAG;IAClB,OAAO,EAAE,aAAa,CAAC;IACvB,MAAM,EAAE,YAAY,CAAC;CACtB,CAAC;AAgLF,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;2BAWzB,MAAM,WAAW,OAAO;;;;;;;;EAwDxD"}
+{"version":3,"file":"scientify-cron.d.ts","sourceRoot":"","sources":["../../../src/tools/scientify-cron.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAA6C,YAAY,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AASvG,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;EAyFlC,CAAC;AAEH,KAAK,YAAY,GAAG;IAClB,OAAO,EAAE,aAAa,CAAC;IACvB,MAAM,EAAE,YAAY,CAAC;CACtB,CAAC;AAwLF,wBAAgB,uBAAuB,CAAC,IAAI,EAAE,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;2BAWzB,MAAM,WAAW,OAAO;;;;;;;;EAuFxD"}

package/dist/src/tools/scientify-cron.js

@@ -48,6 +48,9 @@ export const ScientifyCronToolSchema = Type.Object({
     no_deliver: Type.Optional(Type.Boolean({
         description: "If true, run in background without push delivery.",
     })),
+    run_now: Type.Optional(Type.Boolean({
+        description: "If true (upsert only), trigger one immediate run after job creation/update and return the run result handle.",
+    })),
     job_id: Type.Optional(Type.String({
         description: "Specific job id to remove (only used when action=remove).",
     })),
@@ -103,6 +106,15 @@ function normalizeScope(raw) {
         .replace(/^-|-$/g, "");
     return base || "global";
 }
+function parseJobIdFromResultText(text) {
+    const fenced = text.match(/Job ID:\s*`([^`]+)`/i);
+    if (fenced?.[1])
+        return fenced[1].trim();
+    const plain = text.match(/Job ID:\s*([a-z0-9-]{8,})/i);
+    if (plain?.[1])
+        return plain[1].trim();
+    return undefined;
+}
 function buildToolContext(scope, args, commandBody) {
     return {
         senderId: `tool_${scope}`,
@@ -225,7 +237,27 @@ export function createScientifyCronTool(deps) {
                         return Result.err("operation_failed", err);
                     }
                     const text = getResultText(res);
-                    return Result.ok({ action, scope, result: text });
+                    const jobId = parseJobIdFromResultText(text);
+                    const runNow = readBooleanParam(params, "run_now");
+                    if (runNow && jobId) {
+                        let runRes = await deps.runtime.system.runCommandWithTimeout(["openclaw", "cron", "run", jobId, "--json"], { timeoutMs: 120_000 });
+                        if (runRes.code !== 0 &&
+                            /unknown option '--json'|unknown option \"--json\"|unknown option\s+--json/i.test(runRes.stderr || "")) {
+                            runRes = await deps.runtime.system.runCommandWithTimeout(["openclaw", "cron", "run", jobId], { timeoutMs: 120_000 });
+                        }
+                        if (runRes.code !== 0) {
+                            return Result.err("operation_failed", runRes.stderr || `cron run failed for job ${jobId}`);
+                        }
+                        return Result.ok({
+                            action,
+                            scope,
+                            job_id: jobId,
+                            run_now: true,
+                            run_result: runRes.stdout.trim(),
+                            result: text,
+                        });
+                    }
+                    return Result.ok({ action, scope, ...(jobId ? { job_id: jobId } : {}), result: text });
                 }
                 if (action === "list") {
                     const ctx = buildToolContext(scope, "", "/research-subscriptions");

package/dist/src/tools/scientify-cron.js.map

@@ -1 +1 @@
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package/dist/src/tools/scientify-literature-state.d.ts

@@ -134,6 +134,8 @@ export declare const ScientifyLiteratureStateToolSchema: import("@sinclair/typeb
             error: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
             degraded: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
             notes: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+            required_core_papers: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
+            required_full_text_coverage_pct: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
             temp_full_text_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
             temp_files_downloaded: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
             temp_cleanup_status: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
@@ -283,6 +285,8 @@ export declare function createScientifyLiteratureStateTool(): {
                 error: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
                 degraded: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TBoolean>;
                 notes: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
+                required_core_papers: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
+                required_full_text_coverage_pct: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
                 temp_full_text_dir: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;
                 temp_files_downloaded: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TNumber>;
                 temp_cleanup_status: import("@sinclair/typebox").TOptional<import("@sinclair/typebox").TString>;

package/dist/src/tools/scientify-literature-state.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scientify-literature-state.d.ts","sourceRoot":"","sources":["../../../src/tools/scientify-literature-state.ts"],"names":[],"mappings":"AAkLA,eAAO,MAAM,kCAAkC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8D7C,CAAC;AAqpBH,wBAAgB,kCAAkC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;2BAOjB,MAAM,WAAW,OAAO;;;;;;;;EA2PxD"}
+{"version":3,"file":"scientify-literature-state.d.ts","sourceRoot":"","sources":["../../../src/tools/scientify-literature-state.ts"],"names":[],"mappings":"AAwLA,eAAO,MAAM,kCAAkC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8D7C,CAAC;AAoqBH,wBAAgB,kCAAkC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;2BAOjB,MAAM,WAAW,OAAO;;;;;;;;EA0RxD"}

package/dist/src/tools/scientify-literature-state.js

@@ -101,6 +101,8 @@ const KnowledgeRunLogSchema = Type.Object({
     error: Type.Optional(Type.String({ description: "Optional run error text." })),
     degraded: Type.Optional(Type.Boolean({ description: "Whether this run used degraded behavior." })),
     notes: Type.Optional(Type.String({ description: "Optional extra notes." })),
+    required_core_papers: Type.Optional(Type.Number({ description: "Optional hard requirement for minimum core papers in this run." })),
+    required_full_text_coverage_pct: Type.Optional(Type.Number({ description: "Optional hard requirement for minimum full-text coverage percentage." })),
     temp_full_text_dir: Type.Optional(Type.String({ description: "Temporary local directory for full-text files." })),
     temp_files_downloaded: Type.Optional(Type.Number({ description: "Number of temporary full-text files downloaded." })),
     temp_cleanup_status: Type.Optional(Type.String({
@@ -601,6 +603,14 @@ function readKnowledgeStatePayload(params) {
             const error = typeof runLogRecord.error === "string" ? runLogRecord.error.trim() : undefined;
             const degraded = runLogRecord.degraded === true;
             const notes = typeof runLogRecord.notes === "string" ? runLogRecord.notes.trim() : undefined;
+            const requiredCorePapersRaw = runLogRecord.required_core_papers ?? runLogRecord.requiredCorePapers;
+            const requiredCorePapers = typeof requiredCorePapersRaw === "number" && Number.isFinite(requiredCorePapersRaw)
+                ? Math.max(0, Math.floor(requiredCorePapersRaw))
+                : undefined;
+            const requiredFullTextCoveragePctRaw = runLogRecord.required_full_text_coverage_pct ?? runLogRecord.requiredFullTextCoveragePct;
+            const requiredFullTextCoveragePct = typeof requiredFullTextCoveragePctRaw === "number" && Number.isFinite(requiredFullTextCoveragePctRaw)
+                ? Math.max(0, Math.min(100, Number(requiredFullTextCoveragePctRaw.toFixed(2))))
+                : undefined;
             const tempFullTextDir = typeof (runLogRecord.temp_full_text_dir ?? runLogRecord.tempFullTextDir) === "string"
                 ? String(runLogRecord.temp_full_text_dir ?? runLogRecord.tempFullTextDir).trim()
                 : undefined;
@@ -630,6 +640,8 @@ function readKnowledgeStatePayload(params) {
                 !error &&
                 !degraded &&
                 !notes &&
+                requiredCorePapers === undefined &&
+                requiredFullTextCoveragePct === undefined &&
                 !tempFullTextDir &&
                 tempFilesDownloaded === undefined &&
                 !tempCleanupStatus &&
@@ -644,6 +656,8 @@ function readKnowledgeStatePayload(params) {
                 ...(error ? { error } : {}),
                 ...(degraded ? { degraded } : {}),
                 ...(notes ? { notes } : {}),
+                ...(requiredCorePapers !== undefined ? { requiredCorePapers } : {}),
+                ...(requiredFullTextCoveragePct !== undefined ? { requiredFullTextCoveragePct } : {}),
                 ...(tempFullTextDir ? { tempFullTextDir } : {}),
                 ...(tempFilesDownloaded !== undefined ? { tempFilesDownloaded } : {}),
                 ...(tempCleanupStatus ? { tempCleanupStatus } : {}),
@@ -771,6 +785,7 @@ export function createScientifyLiteratureStateTool() {
                         scope: recorded.scope,
                         topic: recorded.topic,
                         topic_key: recorded.topicKey,
+                        run_id: recorded.runId,
                         preferences: {
                             max_papers: recorded.preferences.maxPapers,
                             recency_days: recorded.preferences.recencyDays,
@@ -805,9 +820,22 @@ export function createScientifyLiteratureStateTool() {
                                     citation_error_rate_pct: recorded.knowledgeStateSummary.qualityGate.citationErrorRatePct,
                                     reasons: recorded.knowledgeStateSummary.qualityGate.reasons,
                                 },
+                                hypothesis_gate: {
+                                    accepted: recorded.knowledgeStateSummary.hypothesisGate.accepted,
+                                    rejected: recorded.knowledgeStateSummary.hypothesisGate.rejected,
+                                    rejection_reasons: recorded.knowledgeStateSummary.hypothesisGate.rejectionReasons,
+                                },
                                 unread_core_paper_ids: recorded.knowledgeStateSummary.unreadCorePaperIds,
                                 last_run_at_ms: recorded.knowledgeStateSummary.lastRunAtMs ?? null,
                                 last_status: recorded.knowledgeStateSummary.lastStatus ?? null,
+                                last_reflection_tasks: recorded.knowledgeStateSummary.lastReflectionTasks.map((task) => ({
+                                    id: task.id,
+                                    trigger: task.trigger,
+                                    reason: task.reason,
+                                    query: task.query,
+                                    priority: task.priority,
+                                    status: task.status,
+                                })),
                                 recent_papers: recorded.knowledgeStateSummary.recentPapers.map(serializeKnowledgePaper),
                             }
                             : null,
@@ -869,6 +897,7 @@ export function createScientifyLiteratureStateTool() {
                         scope: status.scope,
                         topic: status.topic,
                         topic_key: status.topicKey,
+                        latest_run_id: status.recentChangeStats[0]?.runId ?? null,
                         preferences: {
                             max_papers: status.preferences.maxPapers,
                             recency_days: status.preferences.recencyDays,
@@ -887,6 +916,9 @@ export function createScientifyLiteratureStateTool() {
                         total_runs: status.totalRuns,
                         last_status: status.lastStatus ?? null,
                         last_pushed_at_ms: status.lastPushedAtMs ?? null,
+                        knowledge_state_missing_reason: status.knowledgeStateSummary
+                            ? null
+                            : status.knowledgeStateMissingReason ?? "project_or_stream_not_found",
                         knowledge_state_summary: status.knowledgeStateSummary
                             ? {
                                 project_id: status.knowledgeStateSummary.projectId,
@@ -904,9 +936,22 @@ export function createScientifyLiteratureStateTool() {
                                     citation_error_rate_pct: status.knowledgeStateSummary.qualityGate.citationErrorRatePct,
                                     reasons: status.knowledgeStateSummary.qualityGate.reasons,
                                 },
+                                hypothesis_gate: {
+                                    accepted: status.knowledgeStateSummary.hypothesisGate.accepted,
+                                    rejected: status.knowledgeStateSummary.hypothesisGate.rejected,
+                                    rejection_reasons: status.knowledgeStateSummary.hypothesisGate.rejectionReasons,
+                                },
                                 unread_core_paper_ids: status.knowledgeStateSummary.unreadCorePaperIds,
                                 last_run_at_ms: status.knowledgeStateSummary.lastRunAtMs ?? null,
                                 last_status: status.knowledgeStateSummary.lastStatus ?? null,
+                                last_reflection_tasks: status.knowledgeStateSummary.lastReflectionTasks.map((task) => ({
+                                    id: task.id,
+                                    trigger: task.trigger,
+                                    reason: task.reason,
+                                    query: task.query,
+                                    priority: task.priority,
+                                    status: task.status,
+                                })),
                                 recent_papers: status.knowledgeStateSummary.recentPapers.map(serializeKnowledgePaper),
                             }
                             : null,