scientify 1.12.1 → 1.12.2

package/dist/src/commands/metabolism-status.js

@@ -1,100 +1,103 @@
 import * as fs from "node:fs";
 import * as path from "node:path";
 import * as os from "node:os";
-const OPENCLAW_HOME = path.join(os.homedir(), ".openclaw");
-/**
- * Find the research project workspace for the current agent context.
- * In a Feishu group bound to a project agent, the workspace is at
- * ~/.openclaw/workspace-research-{id}/
- */
-function findProjectWorkspace() {
-    // Read openclaw.json to find research agents
-    const configPath = path.join(OPENCLAW_HOME, "openclaw.json");
-    let config;
-    try {
-        config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
-    }
-    catch {
-        return null;
-    }
-    const agents = config.agents?.list ?? [];
-    const researchAgents = agents.filter((a) => a.id.startsWith("research-"));
-    // Try each research agent workspace to find one with metabolism/config.json
-    for (const agent of researchAgents) {
-        const workspace = (agent.workspace ?? `~/.openclaw/workspace-${agent.id}`).replace("~", os.homedir());
-        const metabolismConfig = path.join(workspace, "metabolism", "config.json");
-        if (fs.existsSync(metabolismConfig)) {
-            return { workspace, projectId: agent.id.replace("research-", "") };
-        }
-    }
-    // If only one research agent, use it even without config.json (pre-bootstrap)
-    if (researchAgents.length === 1) {
-        const agent = researchAgents[0];
-        const workspace = (agent.workspace ?? `~/.openclaw/workspace-${agent.id}`).replace("~", os.homedir());
-        return { workspace, projectId: agent.id.replace("research-", "") };
-    }
-    return null;
-}
-function readMetabolismConfig(workspace) {
+const WORKSPACE_ROOT = path.join(os.homedir(), ".openclaw", "workspace", "projects");
+function getActiveProject() {
+    const activePath = path.join(WORKSPACE_ROOT, ".active");
     try {
-        return JSON.parse(fs.readFileSync(path.join(workspace, "metabolism", "config.json"), "utf-8"));
+        return fs.readFileSync(activePath, "utf-8").trim();
     }
     catch {
         return null;
     }
 }
-function countFiles(dirPath, filter) {
+function listProjects() {
     try {
-        const entries = fs.readdirSync(dirPath);
-        return filter ? entries.filter(filter).length : entries.length;
+        return fs
+            .readdirSync(WORKSPACE_ROOT, { withFileTypes: true })
+            .filter((d) => d.isDirectory() && !d.name.startsWith("."))
+            .map((d) => d.name)
+            .sort();
     }
     catch {
-        return 0;
+        return [];
     }
 }
-function readRecentDiffs(workspace, count) {
-    const diffsDir = path.join(workspace, "metabolism", "diffs");
+function readKnowledgeState(projectId) {
+    const file = path.join(WORKSPACE_ROOT, projectId, "knowledge_state", "state.json");
+    if (!fs.existsSync(file))
+        return null;
     try {
-        return fs
-            .readdirSync(diffsDir)
-            .filter((f) => f.endsWith(".md"))
-            .sort()
-            .slice(-count);
+        const raw = fs.readFileSync(file, "utf-8");
+        return JSON.parse(raw);
     }
     catch {
-        return [];
+        return null;
     }
 }
 /**
- * /metabolism-status — Show knowledge metabolism status
+ * /metabolism-status — compatibility alias of continuous research engine status.
  */
-export function handleMetabolismStatus(_ctx) {
-    const project = findProjectWorkspace();
-    if (!project) {
-        return { text: "No research project found. Use `openclaw research init <id>` to create one." };
+export function handleMetabolismStatus(ctx) {
+    const requested = (ctx.args ?? "").trim();
+    const projectId = requested || getActiveProject() || listProjects()[0];
+    if (!projectId) {
+        return {
+            text: "No project found. Use /research-subscribe with --project, or create a project under ~/.openclaw/workspace/projects/.",
+        };
+    }
+    const data = readKnowledgeState(projectId);
+    if (!data?.streams || Object.keys(data.streams).length === 0) {
+        return {
+            text: `**Continuous Research Engine Status — ${projectId}**\n\n` +
+                "No knowledge_state runs yet. Trigger a research run first.\n\n" +
+                "(Compatibility note: /metabolism-status is an alias view over knowledge_state.)",
+        };
+    }
+    const streams = Object.values(data.streams);
+    let totalRuns = 0;
+    let totalHypotheses = 0;
+    let totalPaperNotes = 0;
+    let latest = null;
+    let latestTs = 0;
+    for (const stream of streams) {
+        totalRuns += Number.isFinite(stream.totalRuns) ? Math.max(0, Math.floor(stream.totalRuns)) : 0;
+        totalHypotheses += Number.isFinite(stream.totalHypotheses) ? Math.max(0, Math.floor(stream.totalHypotheses)) : 0;
+        totalPaperNotes += Array.isArray(stream.paperNotes) ? stream.paperNotes.length : 0;
+        const ts = Number.isFinite(stream.lastRunAtMs) ? Math.floor(stream.lastRunAtMs) : 0;
+        if (ts >= latestTs) {
+            latestTs = ts;
+            latest = stream;
+        }
     }
-    const { workspace, projectId } = project;
-    const config = readMetabolismConfig(workspace);
-    const topicCount = countFiles(path.join(workspace, "metabolism", "knowledge"), (f) => f.startsWith("topic-"));
-    const hypothesisCount = countFiles(path.join(workspace, "metabolism", "hypotheses"), (f) => f.endsWith(".md"));
-    const recentDiffs = readRecentDiffs(workspace, 3);
-    let output = `**Metabolism Status — ${projectId}**\n\n`;
-    if (!config) {
-        output += "Status: Pending BOOTSTRAP configuration\n";
-        output += "Send a message in this group to start the configuration flow.\n";
-        return { text: output };
+    const runProfile = latest?.lastRunProfile ?? "fast";
+    const trigger = latest?.triggerState;
+    const gate = latest?.lastQualityGate;
+    let output = `**Continuous Research Engine Status — ${projectId}**\n\n`;
+    output += `- Streams: ${streams.length}\n`;
+    output += `- Total runs: ${totalRuns}\n`;
+    output += `- Total hypotheses: ${totalHypotheses}\n`;
+    output += `- Total paper notes: ${totalPaperNotes}\n`;
+    output += `- Latest run profile: ${runProfile}\n`;
+    output += `- Latest status: ${latest?.lastStatus ?? "(unknown)"}\n`;
+    output += `- Latest run: ${latestTs > 0 ? new Date(latestTs).toISOString() : "(none)"}\n`;
+    if (trigger) {
+        output += `\n**Trigger State**\n`;
+        output += `- Consecutive NEW/REVISE days: ${trigger.consecutiveNewReviseDays ?? 0}\n`;
+        output += `- BRIDGE count (7d): ${trigger.bridgeCount7d ?? 0}\n`;
+        output += `- Unread core backlog: ${trigger.unreadCoreBacklog ?? 0}\n`;
     }
-    const heartbeatStatus = config.heartbeat?.enabled !== false ? "active" : "paused";
-    output += `Day: ${config.currentDay}\n`;
-    output += `Topics: ${topicCount}\n`;
-    output += `Hypotheses: ${hypothesisCount}\n`;
-    output += `Heartbeat: ${heartbeatStatus}\n`;
-    if (recentDiffs.length > 0) {
-        output += `\nRecent diffs:\n`;
-        for (const diff of recentDiffs) {
-            output += `  ${diff}\n`;
+    if (gate) {
+        output += `\n**Quality Gate**\n`;
+        output += `- Passed: ${gate.passed ? "yes" : "no"}\n`;
+        output += `- Full-text coverage: ${gate.fullTextCoveragePct ?? 0}%\n`;
+        output += `- Evidence binding: ${gate.evidenceBindingRatePct ?? 0}%\n`;
+        output += `- Citation error: ${gate.citationErrorRatePct ?? 0}%\n`;
+        if (Array.isArray(gate.reasons) && gate.reasons.length > 0) {
+            output += `- Reasons: ${gate.reasons.join("; ")}\n`;
         }
     }
+    output += "\n(Compatibility note: /metabolism-status is an alias view over knowledge_state.)";
     return { text: output };
 }
 //# sourceMappingURL=metabolism-status.js.map

package/dist/src/commands/metabolism-status.js.map

@@ -1 +1 @@
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+{"version":3,"file":"metabolism-status.js","sourceRoot":"","sources":["../../../src/commands/metabolism-status.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAG9B,MAAM,cAAc,GAAG,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,EAAE,EAAE,WAAW,EAAE,WAAW,EAAE,UAAU,CAAC,CAAC;AA2BrF,SAAS,gBAAgB;IACvB,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,cAAc,EAAE,SAAS,CAAC,CAAC;IACxD,IAAI,CAAC;QACH,OAAO,EAAE,CAAC,YAAY,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC;IACrD,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,SAAS,YAAY;IACnB,IAAI,CAAC;QACH,OAAO,EAAE;aACN,WAAW,CAAC,cAAc,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC;aACpD,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;aACzD,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;aAClB,IAAI,EAAE,CAAC;IACZ,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,CAAC;IACZ,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,SAAiB;IAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,cAAc,EAAE,SAAS,EAAE,iBAAiB,EAAE,YAAY,CAAC,CAAC;IACnF,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IACtC,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,EAAE,CAAC,YAAY,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;QAC3C,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,CAAuB,CAAC;IAC/C,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,sBAAsB,CAAC,GAAyB;IAC9D,MAAM,SAAS,GAAG,CAAC,GAAG,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IAC1C,MAAM,SAAS,GAAG,SAAS,IAAI,gBAAgB,EAAE,IAAI,YAAY,EAAE,CAAC,CAAC,CAAC,CAAC;IACvE,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,OAAO;YACL,IAAI,EAAE,sHAAsH;SAC7H,CAAC;IACJ,CAAC;IAED,MAAM,IAAI,GAAG,kBAAkB,CAAC,SAAS,CAAC,CAAC;IAC3C,IAAI,CAAC,IAAI,EAAE,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7D,OAAO;YACL,IAAI,EACF,yCAAyC,SAAS,QAAQ;gBAC1D,gEAAgE;gBAChE,iFAAiF;SACpF,CAAC;IACJ,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;IAC5C,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,eAAe,GAAG,CAAC,CAAC;IACxB,IAAI,eAAe,GAAG,CAAC,CAAC;IACxB,IAAI,MAAM,GAAuB,IAAI,CAAC;IACtC,IAAI,QAAQ,GAAG,CAAC,CAAC;IAEjB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,SAAS,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,SAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAChG,eAAe,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,eAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAClH,eAAe,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;QACnF,MAAM,EAAE,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,WAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QACrF,IAAI,EAAE,IAAI,QAAQ,EAAE,CAAC;YACnB,QAAQ,GAAG,EAAE,CAAC;YACd,MAAM,GAAG,MAAM,CAAC;QAClB,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,MAAM,EAAE,cAAc,IAAI,MAAM,CAAC;IACpD,MAAM,OAAO,GAAG,MAAM,EAAE,YAAY,CAAC;IACrC,MAAM,IAAI,GAAG,MAAM,EAAE,eAAe,CAAC;IAErC,IAAI,MAAM,GAAG,yCAAyC,SAAS,QAAQ,CAAC;IACxE,MAAM,IAAI,cAAc,OAAO,CAAC,MAAM,IAAI,CAAC;IAC3C,MAAM,IAAI,iBAAiB,SAAS,IAAI,CAAC;IACzC,MAAM,IAAI,uBAAuB,eAAe,IAAI,CAAC;IACrD,MAAM,IAAI,wBAAwB,eAAe,IAAI,CAAC;IACtD,MAAM,IAAI,yBAAyB,UAAU,IAAI,CAAC;IAClD,MAAM,IAAI,oBAAoB,MAAM,EAAE,UAAU,IAAI,WAAW,IAAI,CAAC;IACpE,MAAM,IAAI,iBAAiB,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC;IAE1F,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,uBAAuB,CAAC;QAClC,MAAM,IAAI,kCAAkC,OAAO,CAAC,wBAAwB,IAAI,CAAC,IAAI,CAAC;QACtF,MAAM,IAAI,wBAAwB,OAAO,CAAC,aAAa,IAAI,CAAC,IAAI,CAAC;QACjE,MAAM,IAAI,0BAA0B,OAAO,CAAC,iBAAiB,IAAI,CAAC,IAAI,CAAC;IACzE,CAAC;IAED,IAAI,IAAI,EAAE,CAAC;QACT,MAAM,IAAI,sBAAsB,CAAC;QACjC,MAAM,IAAI,aAAa,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC;QACtD,MAAM,IAAI,yBAAyB,IAAI,CAAC,mBAAmB,IAAI,CAAC,KAAK,CAAC;QACtE,MAAM,IAAI,uBAAuB,IAAI,CAAC,sBAAsB,IAAI,CAAC,KAAK,CAAC;QACvE,MAAM,IAAI,qBAAqB,IAAI,CAAC,oBAAoB,IAAI,CAAC,KAAK,CAAC;QACnE,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3D,MAAM,IAAI,cAAc,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;QACtD,CAAC;IACH,CAAC;IAED,MAAM,IAAI,mFAAmF,CAAC;IAC9F,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;AAC1B,CAAC"}

package/dist/src/commands.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/commands.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AAwJ1E;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAmDpF;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAiC3E;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA4B1E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAqB9E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAclF;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA+ClF"}
+{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/commands.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AA6N1E;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CA+DpF;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAiC3E;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA4B1E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAqB9E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAclF;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA+ClF"}

package/dist/src/commands.js

@@ -92,6 +92,9 @@ function getKnowledgeStateSummary(projectId) {
         let recentNotFullTextReadCount = 0;
         let lastRunAtMs = 0;
         let lastStatus;
+        let lastQualityGatePassed;
+        let lastQualityGateReasons;
+        let lastChangeStat;
         for (const stream of streamEntries) {
             totalRuns += Number.isFinite(stream.totalRuns) ? Math.max(0, Math.floor(stream.totalRuns)) : 0;
             totalHypotheses += Number.isFinite(stream.totalHypotheses)
@@ -108,6 +111,43 @@ function getKnowledgeStateSummary(projectId) {
             if (runAt >= lastRunAtMs) {
                 lastRunAtMs = runAt;
                 lastStatus = stream.lastStatus;
+                if (stream.lastQualityGate && typeof stream.lastQualityGate === "object") {
+                    lastQualityGatePassed = stream.lastQualityGate.passed === true;
+                    if (Array.isArray(stream.lastQualityGate.reasons)) {
+                        lastQualityGateReasons = stream.lastQualityGate.reasons
+                            .filter((item) => typeof item === "string")
+                            .map((item) => item.trim())
+                            .filter((item) => item.length > 0)
+                            .slice(0, 5);
+                    }
+                    else {
+                        lastQualityGateReasons = undefined;
+                    }
+                }
+                else {
+                    lastQualityGatePassed = undefined;
+                    lastQualityGateReasons = undefined;
+                }
+                const firstChange = Array.isArray(stream.recentChangeStats) ? stream.recentChangeStats[0] : undefined;
+                if (firstChange && typeof firstChange === "object") {
+                    lastChangeStat = {
+                        newCount: typeof firstChange.newCount === "number" && Number.isFinite(firstChange.newCount)
+                            ? Math.max(0, Math.floor(firstChange.newCount))
+                            : 0,
+                        confirmCount: typeof firstChange.confirmCount === "number" && Number.isFinite(firstChange.confirmCount)
+                            ? Math.max(0, Math.floor(firstChange.confirmCount))
+                            : 0,
+                        reviseCount: typeof firstChange.reviseCount === "number" && Number.isFinite(firstChange.reviseCount)
+                            ? Math.max(0, Math.floor(firstChange.reviseCount))
+                            : 0,
+                        bridgeCount: typeof firstChange.bridgeCount === "number" && Number.isFinite(firstChange.bridgeCount)
+                            ? Math.max(0, Math.floor(firstChange.bridgeCount))
+                            : 0,
+                    };
+                }
+                else {
+                    lastChangeStat = undefined;
+                }
             }
         }
         return {
@@ -116,6 +156,9 @@ function getKnowledgeStateSummary(projectId) {
             totalPaperNotes,
             recentFullTextReadCount,
             recentNotFullTextReadCount,
+            ...(typeof lastQualityGatePassed === "boolean" ? { lastQualityGatePassed } : {}),
+            ...(lastQualityGateReasons && lastQualityGateReasons.length > 0 ? { lastQualityGateReasons } : {}),
+            ...(lastChangeStat ? { lastChangeStat } : {}),
             ...(lastRunAtMs > 0 ? { lastRunAtMs } : {}),
             ...(lastStatus ? { lastStatus } : {}),
             streamCount: streamEntries.length,
@@ -145,6 +188,18 @@ export function handleResearchStatus(_ctx) {
             output += `- recent full-text-read papers: ${knowledgeSummary.recentFullTextReadCount}\n`;
             output += `- recent not-full-text-read papers: ${knowledgeSummary.recentNotFullTextReadCount}\n`;
             output += `- last status: ${knowledgeSummary.lastStatus ?? "(unknown)"}\n`;
+            if (typeof knowledgeSummary.lastQualityGatePassed === "boolean") {
+                output += `- quality gate: ${knowledgeSummary.lastQualityGatePassed ? "passed" : "failed"}\n`;
+            }
+            if (knowledgeSummary.lastQualityGateReasons && knowledgeSummary.lastQualityGateReasons.length > 0) {
+                output += `- quality reasons: ${knowledgeSummary.lastQualityGateReasons.join("; ")}\n`;
+            }
+            if (knowledgeSummary.lastChangeStat) {
+                output +=
+                    `- last change stats (NEW/CONFIRM/REVISE/BRIDGE): ` +
+                        `${knowledgeSummary.lastChangeStat.newCount}/${knowledgeSummary.lastChangeStat.confirmCount}/` +
+                        `${knowledgeSummary.lastChangeStat.reviseCount}/${knowledgeSummary.lastChangeStat.bridgeCount}\n`;
+            }
             output += `- last run: ${knowledgeSummary.lastRunAtMs ? new Date(knowledgeSummary.lastRunAtMs).toISOString() : "(none)"}\n\n`;
         }
     }

package/dist/src/commands.js.map

@@ -1 +1 @@
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package/dist/src/hooks/research-mode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAoDF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,SAAS,WAAW,KAAG,UAAU,CAO7D"}
+{"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAqEF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,SAAS,WAAW,KAAG,UAAU,CAO7D"}

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

@@ -2,43 +2,60 @@
  * Research mode prompt injected into every conversation.
  */
 const RESEARCH_MODE_PROMPT = `[Scientify]
-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).
-no_deliver only disables delivery; it never disables scientify_literature_state.record.
-Do not claim a research cycle is completed unless record returned success.
-When calling scientify_literature_state.record, always set a unique run_id per cycle (cron run id preferred; otherwise timestamp-based id) to avoid idempotent no-op writes.
-Reuse prepare output for state writes: record/status must use the same scope/topic returned by scientify_literature_state.prepare; never swap scope with project_id.
-Execution truth policy: do not claim "running in background", "continue later", or "come back in a few minutes" unless you actually created a real async handle (cron job id from scientify_cron_job or task id from sessions_spawn).
-If no async handle exists, treat it as synchronous: complete prepare -> record -> status in the same turn and report run_id/latest_run_id.
-If you cannot finish a requested run in this turn and you also cannot create a real async handle, state clearly that it is not executed yet; never imply progress that did not happen.
-Long-run fallback policy: when strict quality gates/full-text workload make single-turn completion impractical, start real execution immediately and return a real handle id.
-If user forbids schedule creation, prefer sessions_spawn and return task id.
-Otherwise use scientify_cron_job (upsert + run_now=true) and return job_id.
-Do not end with "not executed" if an async handle can be created.
-Reflection policy: when BRIDGE signal (or REVISE+CONFIRM contradiction signal) appears in knowledge_changes, run at least one immediate reflection query and write it into exploration_trace with query/reason/source/candidates/filtered_to.
-Bridge policy: do not emit BRIDGE unless evidence_ids resolve to this run's papers and include at least one full-text-backed paper.
-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.
-Hard-constraint policy: if user specifies explicit hard targets (for example exact/min core paper count), do not report status ok unless those targets are satisfied; otherwise status should be degraded_quality with unmet reasons.
-Hypothesis gate: avoid speculative ideas. Each hypothesis should include >=2 evidence_ids, dependency_path length >=2, and novelty/feasibility/impact scores, with evidence linked to current run papers.
-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.`;
+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.
+
+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.
+  - Never skip persistence due quality limits; persist degraded/error run with reasons instead.
+  - User-facing responses should be concise Markdown. Keep tool-call JSON minimal and only for persistence.
+  - If strict constraints cannot be fully met in this turn, do not refuse execution; fallback to degraded_quality and persist the run with unmet reasons.
+
+Research quality and gating:
+  - Full-text-first for core evidence papers.
+  - If full text unavailable: set full_text_read=false and unread_reason.
+  - 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 or revise/confirm contradiction appears, include at least one reflection trace item.
+  - Hypotheses are accepted only when evidence_ids and dependency_path are sufficient; otherwise reject via hypothesis_gate reasons.
+  - 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.

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

@@ -1 +1 @@
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+{"version":3,"file":"research-mode.js","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAmBA;;GAEG;AACH,MAAM,oBAAoB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6EAsDgD,CAAC;AAE9E,MAAM,kBAAkB,GAAG;;;;;;qHAM0F,CAAC;AAEtH;;GAEG;AACH,MAAM,UAAU,sBAAsB;IACpC,OAAO,CAAC,MAAiB,EAAE,OAAoB,EAAc,EAAE;QAC7D,MAAM,UAAU,GAAG,OAAO,OAAO,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;QACpF,MAAM,aAAa,GAAG,UAAU,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;QACpD,OAAO;YACL,cAAc,EAAE,aAAa,CAAC,CAAC,CAAC,GAAG,oBAAoB,KAAK,kBAAkB,EAAE,CAAC,CAAC,CAAC,oBAAoB;SACxG,CAAC;IACJ,CAAC,CAAC;AACJ,CAAC"}

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;IACrB,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;AAmGF,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

@@ -11,16 +11,19 @@ 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-survey|research-plan|research-implement|research-review|research-experiment|literature-survey|write-review-paper|research-subscription)(?:\s|$)/i;
+const SCIENTIFY_SKILL_COMMAND_RE = /(?:^|\s)\/(idea-generation|research-pipeline|research-collect|research-survey|research-plan|research-implement|research-review|research-experiment|write-review-paper|research-subscription|research-subscribe|research-subscriptions|research-unsubscribe|metabolism|metabolism-init|metabolism-status)(?:\s|$)/i;
 const 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

@@ -49,6 +49,7 @@ export declare function renderHypothesisMarkdown(args: {
 export declare function renderKnowledgeIndexMarkdown(args: {
     now: string;
     topic: string;
+    runProfile: "fast" | "strict";
     topicFiles: string[];
     paperNotesCount: number;
     totalHypotheses: number;

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

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