nexus-prime 4.3.2 → 4.4.0

package/dist/engines/ngram-index.js.map

@@ -1 +1 @@
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package/dist/engines/orchestrator.d.ts

@@ -102,7 +102,7 @@ export interface SessionBootstrapResult {
     artifactSelectionAudit: RuntimeArtifactSelectionAudit;
     taskGraphPreview: RuntimeTaskGraphSnapshot;
     workerPlanPreview: RuntimeWorkerPlanSnapshot;
-    knowledgeFabric?: {
+    knowledgeFabric: {
         summary: string;
         dominantSource: string;
         attachedCollections: string[];
@@ -206,6 +206,8 @@ export declare class OrchestratorEngine {
     private loadSessionState;
     private persistSessionState;
     private sessionStatePath;
+    /** Remove autonomy-session files older than 14 days */
+    private pruneStaleAutonomySessions;
     private resolvePrimaryClient;
     private listDetectedClients;
     private detectCurrentClientFromEnv;

package/dist/engines/orchestrator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../src/engines/orchestrator.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAI3C,OAAO,EAAqB,KAAK,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAGtE,OAAO,EAAO,KAAK,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAGhE,OAAO,KAAK,EACV,6BAA6B,EAE7B,4BAA4B,EAG5B,wBAAwB,EACxB,4BAA4B,EAC5B,4BAA4B,EAE5B,2BAA2B,EAC3B,yBAAyB,EAC1B,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,iBAAiB,EAAmB,MAAM,kBAAkB,CAAC;AACtE,OAAO,KAAK,EAAgB,cAAc,EAAE,MAAM,sBAAsB,CAAC;AASzE,OAAO,EAAyB,KAAK,uBAAuB,EAAE,MAAM,uBAAuB,CAAC;AAC5F,OAAO,EAEL,KAAK,YAAY,EACjB,KAAK,aAAa,EAClB,KAAK,eAAe,EACrB,MAAM,qBAAqB,CAAC;AAE7B,MAAM,MAAM,SAAS,GAAG,YAAY,GAAG,OAAO,GAAG,SAAS,GAAG,UAAU,GAAG,UAAU,GAAG,WAAW,GAAG,cAAc,CAAC;AAEpH,MAAM,WAAW,KAAK;IACpB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,SAAS,GAAG,MAAM,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,SAAS,GAAG,SAAS,GAAG,UAAU,GAAG,QAAQ,CAAC;IACrD,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,cAAc,CAAC;CAC5B;AAED,MAAM,WAAW,IAAI;IACnB,EAAE,EAAE,MAAM,CAAC;IACX,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,QAAQ,GAAG,SAAS,GAAG,SAAS,GAAG,QAAQ,GAAG,UAAU,GAAG,UAAU,GAAG,KAAK,GAAG,IAAI,GAAG,MAAM,GAAG,UAAU,GAAG,SAAS,GAAG,IAAI,GAAG,WAAW,GAAG,OAAO,GAAG,MAAM,CAAC;IACzK,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACtC,SAAS,EAAE,KAAK,GAAG,QAAQ,GAAG,MAAM,CAAC;IACrC,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC;IACnB,gBAAgB,EAAE,MAAM,EAAE,CAAC;IAC3B,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,IAAI,EAAE,4BAA4B,CAAC,MAAM,CAAC,CAAC;IAC3C,gBAAgB,EAAE,MAAM,CAAC;IACzB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,MAAM,EAAE,cAAc,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,mBAAmB,EAAE,MAAM,EAAE,CAAC;IAC9B,iBAAiB,EAAE,MAAM,EAAE,CAAC;IAC5B,gBAAgB,CAAC,EAAE;QACjB,SAAS,EAAE,MAAM,CAAC;QAClB,SAAS,EAAE,MAAM,CAAC;QAClB,aAAa,EAAE,MAAM,CAAC;KACvB,CAAC;IACF,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,aAAa,CAAC,EAAE,4BAA4B,CAAC;IAC7C,YAAY,CAAC,EAAE,2BAA2B,CAAC;IAC3C,sBAAsB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACjD;AAED,MAAM,WAAW,sBAAsB;IACrC,MAAM,CAAC,EAAE,4BAA4B,CAAC;IACtC,YAAY,EAAE;QACZ,KAAK,EAAE,MAAM,CAAC;QACd,OAAO,EAAE,MAAM,EAAE,CAAC;KACnB,CAAC;IACF,WAAW,EAAE,UAAU,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAC;IAClD,mBAAmB,EAAE,mBAAmB,GAAG,sBAAsB,CAAC;IAClE,wBAAwB,EAAE,4BAA4B,CAAC,MAAM,CAAC,CAAC;IAC/D,SAAS,EAAE;QACT,KAAK,EAAE,MAAM,EAAE,CAAC;QAChB,WAAW,EAAE,MAAM,EAAE,CAAC;QACtB,MAAM,EAAE,MAAM,EAAE,CAAC;QACjB,SAAS,EAAE,MAAM,EAAE,CAAC;QACpB,KAAK,EAAE,MAAM,EAAE,CAAC;QAChB,WAAW,EAAE,MAAM,EAAE,CAAC;KACvB,CAAC;IACF,iBAAiB,EAAE;QACjB,QAAQ,EAAE,OAAO,CAAC;QAClB,MAAM,EAAE,MAAM,CAAC;QACf,cAAc,EAAE,MAAM,EAAE,CAAC;KAC1B,CAAC;IACF,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,aAAa,EAAE,4BAA4B,CAAC;IAC5C,uBAAuB,EAAE;QACvB,cAAc,EAAE,MAAM,CAAC;QACvB,OAAO,EAAE,MAAM,EAAE,CAAC;KACnB,CAAC;IACF,kBAAkB,EAAE;QAClB,mBAAmB,EAAE,MAAM,CAAC;QAC5B,eAAe,EAAE,MAAM,CAAC;QACxB,cAAc,EAAE,MAAM,CAAC;QACvB,aAAa,EAAE,MAAM,CAAC;QACtB,aAAa,EAAE,MAAM,EAAE,CAAC;KACzB,CAAC;IACF,qBAAqB,CAAC,EAAE,uBAAuB,CAAC;IAChD,sBAAsB,EAAE,6BAA6B,CAAC;IACtD,gBAAgB,EAAE,wBAAwB,CAAC;IAC3C,iBAAiB,EAAE,yBAAyB,CAAC;IAC7C,eAAe,EAAE;QACf,OAAO,EAAE,MAAM,CAAC;QAChB,cAAc,EAAE,MAAM,CAAC;QACvB,mBAAmB,EAAE,MAAM,EAAE,CAAC;QAC9B,WAAW,EAAE,MAAM,EAAE,CAAC;QACtB,aAAa,EAAE,MAAM,EAAE,CAAC;QACxB,UAAU,EAAE,MAAM,EAAE,CAAC;KACtB,CAAC;IACF,QAAQ,CAAC,EAAE,YAAY,CAAC;CACzB;AAuCD,UAAU,mBAAmB;IAC3B,MAAM,CAAC,EAAE,YAAY,CAAC;IACtB,OAAO,CAAC,EAAE,eAAe,CAAC;IAC1B,cAAc,CAAC,EAAE,cAAc,CAAC;IAChC,UAAU,CAAC,EAAE,iBAAiB,CAAC;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAQD,qBAAa,kBAAkB;IAC7B,OAAO,CAAC,MAAM,CAAiC;IAC/C,OAAO,CAAC,MAAM,CAAe;IAC7B,OAAO,CAAC,YAAY,CAAK;IACzB,OAAO,CAAC,OAAO,CAAkB;IACjC,OAAO,CAAC,OAAO,CAA6B;IAC5C,OAAO,CAAC,cAAc,CAAC,CAAiB;IACxC,OAAO,CAAC,UAAU,CAAC,CAAoB;IACvC,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,WAAW,CAAuB;IAC1C,OAAO,CAAC,kBAAkB,CAAqB;IAC/C,OAAO,CAAC,eAAe,CAAwB;IAC/C,OAAO,CAAC,WAAW,CAAS;IAC5B,OAAO,CAAC,YAAY,CAAuB;IAC3C,OAAO,CAAC,aAAa,CAAC,CAAiB;IACvC,OAAO,CAAC,kBAAkB,CAAC,CAAqB;IAChD,OAAO,CAAC,sBAAsB,CAAC,CAAyB;IACxD,OAAO,CAAC,wBAAwB,CAAC,CAAa;IAC9C,OAAO,CAAC,iBAAiB,CAAoB;IAC7C,OAAO,CAAC,YAAY,CAAe;IACnC,OAAO,CAAC,YAAY,CAAqB;IACzC,OAAO,CAAC,oBAAoB,CAAiG;IAC7H,OAAO,CAAC,gBAAgB,CAAK;IAC7B,OAAO,CAAC,mBAAmB,CAAK;IAChC,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAK;IACvC,OAAO,CAAC,QAAQ,CAAC,mBAAmB,CAAU;gBAElC,OAAO,GAAE,mBAAwB;IAqC7C;;;OAGG;IACU,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,EAAE,CAAC;IAqB5C,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE;YAe9B,iBAAiB;IAkF/B,OAAO,CAAC,YAAY;IAcpB,OAAO,CAAC,iBAAiB;IASzB,OAAO,CAAC,2BAA2B;IAYnC,OAAO,CAAC,eAAe;IAIvB,OAAO,CAAC,oBAAoB;IAM5B,OAAO,CAAC,kBAAkB;IAkBnB,eAAe,IAAI,YAAY;IAI/B,OAAO,IAAI,IAAI;IAcT,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,OAAO,CAAC,aAAa,CAAM,GAAG,OAAO,CAAC,sBAAsB,CAAC;IAwKlH,OAAO,CAAC,8BAA8B;IAoBzB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,GAAE,OAAO,C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package/dist/engines/orchestrator.js

@@ -5,6 +5,7 @@
  * Raw prompts flow through this layer before the runtime executes work.
  */
 import * as fs from 'fs';
+import * as os from 'os';
 import * as path from 'path';
 import { createHash, randomUUID } from 'crypto';
 import { MemoryEngine } from './memory.js';
@@ -24,6 +25,7 @@ import { readBootstrapManifest } from './client-bootstrap.js';
 import { createSubAgentRuntime, } from '../phantom/index.js';
 const MAX_AUTONOMY_HISTORY = 24;
 const MAX_DISCOVERED_FILES = 32;
+const ABSOLUTE_SECONDARY_MIN = 0.3;
 const DISCOVERY_EXTENSIONS = new Set(['.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs', '.json', '.md', '.yml', '.yaml']);
 const DISCOVERY_IGNORES = new Set(['.git', 'node_modules', 'dist', 'coverage', '.next', '.playwright-cli', 'tmp']);
 export class OrchestratorEngine {
@@ -71,8 +73,20 @@ export class OrchestratorEngine {
             tokenEngine: this.tokenEngine,
         });
         this.sessionsDir = path.join(resolveNexusStateDir(), 'autonomy-sessions');
-        fs.mkdirSync(this.sessionsDir, { recursive: true });
+        try {
+            fs.mkdirSync(this.sessionsDir, { recursive: true });
+        }
+        catch (err) {
+            if (['EROFS', 'ENOENT', 'EACCES'].includes(err?.code)) {
+                this.sessionsDir = path.join(os.tmpdir(), 'nexus-prime-sessions');
+                fs.mkdirSync(this.sessionsDir, { recursive: true });
+            }
+            else {
+                throw err;
+            }
+        }
         this.sessionState = this.loadSessionState();
+        this.pruneStaleAutonomySessions();
         this.memoryBackgroundWorker = new MemoryBackgroundWorker(this.memory);
         this.repoTreeGenerator = new RepoTreeGenerator(this.repoRoot);
         this.skillLearner = new SkillLearnerEngine(this.skillRuntime, this.memory);
@@ -117,17 +131,34 @@ export class OrchestratorEngine {
         const primaryClient = this.resolvePrimaryClient();
         const bootstrapManifest = readBootstrapManifest();
         const latestDNA = SessionDNAManager.loadLatest();
-        const memoryMatches = await this.memory.recall(task, 8, this.buildWorkspaceRecallFilters());
+        const memoryMatchesFull = await this.memory.recallWithMetadata(task, 8, this.buildWorkspaceRecallFilters());
+        const memoryMatches = memoryMatchesFull.map(m => m.content);
         const memoryStats = this.memory.getStats();
         const candidateFiles = options.files?.length
             ? options.files
-            : this.discoverCandidateFiles(task);
+            : this.discoverCandidateFiles(task, latestDNA);
         await this.knowledgeFabric.ensureBootstrapCollection({
             runtimeId: this.runtime.getRuntimeId(),
             sessionId: this.sessionState.sessionId,
             candidateFiles,
         });
-        const knowledgeFabric = this.composeKnowledgeFabric(task, candidateFiles, memoryMatches, intent);
+        let knowledgeFabric;
+        try {
+            const qualityMeta = memoryMatchesFull.map(m => ({ content: m.content, confidence: m.confidence, entropy: m.entropy, trust: m.trust }));
+            const fileBoosts = this.memory.getFileBoosts(candidateFiles);
+            knowledgeFabric = this.composeKnowledgeFabric(task, candidateFiles, memoryMatches, intent, qualityMeta, fileBoosts);
+        }
+        catch (error) {
+            console.warn('[Orchestrator] Knowledge Fabric compose failed, retrying:', error?.message ?? error);
+            try {
+                const qualityMeta = memoryMatchesFull.map(m => ({ content: m.content, confidence: m.confidence, entropy: m.entropy, trust: m.trust }));
+                const fileBoosts = this.memory.getFileBoosts(candidateFiles);
+                knowledgeFabric = this.composeKnowledgeFabric(task, candidateFiles, memoryMatches, intent, qualityMeta, fileBoosts);
+            }
+            catch (retryError) {
+                throw new Error(`[Orchestrator] Knowledge Fabric unavailable: ${retryError?.message ?? retryError}`);
+            }
+        }
         const plannedFiles = options.files?.length
             ? options.files
             : (knowledgeFabric.repo.selectedFiles.length > 0 ? knowledgeFabric.repo.selectedFiles : candidateFiles);
@@ -242,7 +273,11 @@ export class OrchestratorEngine {
         nexusEventBus.emit('orchestrator.disposed', { ts: Date.now() });
     }
     async bootstrapSession(task, options = {}) {
-        const prepared = await this._prepareExecution(task, options);
+        const prepared = await new Promise((resolve, reject) => {
+            setImmediate(() => {
+                this._prepareExecution(task, options).then(resolve, reject);
+            });
+        });
         const { intent, phases, primaryClient, bootstrapManifest, latestDNA, memoryMatches, memoryStats, knowledgeFabric, planner, selections, catalogHealth, tokenBudget, mode, taskGraph, workerPlan, } = prepared;
         const tokenOptimizationRequired = true; // MUST run mandatorily
         const ragUsageSummary = this.toRagUsageSummary(knowledgeFabric, {
@@ -671,6 +706,14 @@ export class OrchestratorEngine {
                 state: 'failed',
                 ts: Date.now(),
             });
+            setTimeout(() => this.executionDedupeStore.delete(fingerprint), 120_000).unref();
+            const envErrors = ['EROFS', 'ENOENT', 'EACCES', 'EPERM'];
+            if (envErrors.includes(error?.code)) {
+                console.error('[Orchestrator] Env error (not orchestration failure):', error.code);
+            }
+            else {
+                this.updateCircuitState('failed');
+            }
             throw error;
         }
         this.executionDedupeStore.set(fingerprint, {
@@ -678,6 +721,7 @@ export class OrchestratorEngine {
             state: run.state,
             ts: Date.now(),
         });
+        setTimeout(() => this.executionDedupeStore.delete(fingerprint), 120_000).unref();
         this.lastRun = run;
         const artifactOutcome = this.buildArtifactOutcome(selections.audit, run);
         army.forEach((agent) => {
@@ -700,6 +744,17 @@ export class OrchestratorEngine {
             selectedAutomations: run.activeAutomations.map((automation) => automation.name),
         };
         this.persistSessionState();
+        try {
+            if (tokenPlan) {
+                const { accumulateLifetimeTokens } = await import('./lifetime-tokens.js');
+                accumulateLifetimeTokens({
+                    savedTokens: tokenPlan.savings ?? 0,
+                    grossInputTokens: (tokenPlan.totalEstimatedTokens ?? 0) + (tokenPlan.savings ?? 0),
+                    compressedTokens: tokenPlan.totalEstimatedTokens ?? 0,
+                });
+            }
+        }
+        catch { /* non-critical */ }
         this.runtime.recordOrchestrationSnapshot(this.toRuntimeOrchestrationSnapshot(this.sessionState));
         this.runtime.recordPrimaryClient(primaryClient, this.listDetectedClients());
         this.runtime.recordArtifactOutcome(artifactOutcome);
@@ -817,13 +872,15 @@ export class OrchestratorEngine {
             workers: options?.workers,
         });
     }
-    composeKnowledgeFabric(task, candidateFiles, memoryMatches, intent) {
+    composeKnowledgeFabric(task, candidateFiles, memoryMatches, intent, memoryMatchesFull, fileBoosts) {
         const bundle = this.knowledgeFabric.compose({
             runtimeId: this.runtime.getRuntimeId(),
             sessionId: this.sessionState.sessionId,
             task,
             candidateFiles,
             memoryMatches,
+            memoryMatchesWithQuality: memoryMatchesFull,
+            fileBoosts,
             runtimeSnapshot: this.runtime.getUsageSnapshot(),
             intent,
         });
@@ -837,7 +894,14 @@ export class OrchestratorEngine {
                 return JSON.parse(fs.readFileSync(target, 'utf8'));
             }
             catch {
-                // fall through to new state
+                const corruptPath = target.replace(/\.json$/, `.corrupt-${Date.now()}.json`);
+                try {
+                    fs.copyFileSync(target, corruptPath);
+                }
+                catch {
+                    // ignore backup failures
+                }
+                console.error('[Orchestrator] Corrupt session file backed up to:', corruptPath);
             }
         }
         const sessionId = this.sessionDNA?.getSessionId?.() ?? `autonomy-${randomUUID().slice(0, 8)}`;
@@ -863,11 +927,36 @@ export class OrchestratorEngine {
         };
     }
     persistSessionState() {
-        fs.writeFileSync(this.sessionStatePath(), JSON.stringify(this.sessionState, null, 2), 'utf8');
+        try {
+            fs.writeFileSync(this.sessionStatePath(), JSON.stringify(this.sessionState, null, 2), 'utf8');
+        }
+        catch (err) {
+            console.error('[Orchestrator] Failed to persist session state:', err?.message);
+        }
     }
     sessionStatePath() {
         return path.join(this.sessionsDir, `${this.runtime.getRuntimeId()}.json`);
     }
+    /** Remove autonomy-session files older than 14 days */
+    pruneStaleAutonomySessions() {
+        try {
+            const TTL_MS = 14 * 24 * 60 * 60 * 1000;
+            const now = Date.now();
+            for (const entry of fs.readdirSync(this.sessionsDir)) {
+                if (!entry.endsWith('.json'))
+                    continue;
+                const filePath = path.join(this.sessionsDir, entry);
+                try {
+                    const stat = fs.statSync(filePath);
+                    if (now - stat.mtimeMs > TTL_MS) {
+                        fs.unlinkSync(filePath);
+                    }
+                }
+                catch { /* best-effort */ }
+            }
+        }
+        catch { /* best-effort */ }
+    }
     resolvePrimaryClient() {
         const primary = this.clientRegistry?.getPrimaryClient?.();
         if (primary)
@@ -1077,7 +1166,8 @@ export class OrchestratorEngine {
         const bestScore = sorted[0]?.[1] ?? 0;
         // Secondary intent: if 2nd place score >= 80% of 1st place, it's a meaningful secondary signal
         const secondaryThreshold = isTechnicalAudit ? 0.45 : 0.8;
-        const secondaryType = sorted[1]?.[1] > 0 && bestScore > 0 && sorted[1][1] >= bestScore * secondaryThreshold
+        const threshold = Math.max(secondaryThreshold * bestScore, ABSOLUTE_SECONDARY_MIN);
+        const secondaryType = sorted[1]?.[1] > 0 && bestScore > 0 && sorted[1][1] >= threshold
             ? sorted[1][0]
             : undefined;
         const taskType = bestIntent;
@@ -1110,12 +1200,19 @@ export class OrchestratorEngine {
         const complexity = Math.max(1, Math.min(6, this.decomposeTask(task).length + (task.length > 120 ? 1 : 0) + (riskClass === 'high' ? 1 : 0)));
         return { taskType, secondaryType, intentScores, riskClass, complexity };
     }
-    discoverCandidateFiles(task) {
+    discoverCandidateFiles(task, dna) {
         const keywords = extractKeywords(task);
+        // Build a set of files from previous session DNA for boosting
+        const dnaFiles = new Set();
+        if (dna) {
+            for (const f of [...(dna.filesAccessed ?? []), ...(dna.filesModified ?? [])]) {
+                dnaFiles.add(f);
+            }
+        }
         const candidates = this.walkRepo(this.repoRoot)
             .map((filePath) => ({
             filePath,
-            score: scorePath(filePath, keywords),
+            score: scorePath(filePath, keywords) + (dnaFiles.has(filePath) ? 0.3 : 0),
         }))
             .filter((entry) => entry.score > 0)
             .sort((left, right) => right.score - left.score || left.filePath.localeCompare(right.filePath))
@@ -1124,8 +1221,18 @@ export class OrchestratorEngine {
         if (candidates.length > 0) {
             return candidates;
         }
-        return ['README.md', 'AGENTS.md', 'package.json']
-            .map((entry) => path.join(this.repoRoot, entry))
+        const srcFiles = (() => {
+            try {
+                return fs.readdirSync(path.join(this.repoRoot, 'src'))
+                    .filter((entry) => entry.endsWith('.ts'))
+                    .map((entry) => path.join(this.repoRoot, 'src', entry));
+            }
+            catch {
+                return [];
+            }
+        })();
+        return ['README.md', 'package.json', ...srcFiles]
+            .map((entry) => entry.startsWith(this.repoRoot) ? entry : path.join(this.repoRoot, entry))
             .filter((entry) => fs.existsSync(entry));
     }
     walkRepo(root, seen = []) {
@@ -1376,7 +1483,7 @@ export class OrchestratorEngine {
             return true;
         if (entry.source === 'knowledge-fabric')
             return entry.score >= 0.72 || entry.confidence !== 'low';
-        return entry.confidence !== 'low' && entry.score >= 0.64;
+        return entry.score > 0;
     }
     toArtifactAuditEntry(kind, value, items, input, selected = true) {
         const item = items.find((entry) => (input.selector === 'id' ? entry.id === value : entry.name === value));
@@ -1406,23 +1513,38 @@ export class OrchestratorEngine {
             .slice(0, limit);
     }
     scanCatalogHealth(selections) {
-        const scanLocalDirectory = (relativeDir) => {
-            const localDirectory = path.join(this.repoRoot, relativeDir);
-            if (!fs.existsSync(localDirectory)) {
-                return { localDirectory, readable: false, files: 0, issues: [`Missing ${relativeDir}`] };
-            }
-            try {
-                const files = fs.readdirSync(localDirectory).filter((entry) => !entry.startsWith('.')).length;
-                return { localDirectory, readable: true, files, issues: [] };
-            }
-            catch {
-                return { localDirectory, readable: false, files: 0, issues: [`Unreadable ${relativeDir}`] };
-            }
+        const scanLocalDirectories = (relativeDirs) => {
+            const scanned = relativeDirs.map((relativeDir) => {
+                const localDirectory = path.join(this.repoRoot, relativeDir);
+                if (!fs.existsSync(localDirectory)) {
+                    return { relativeDir, localDirectory, readable: false, files: 0, issues: [] };
+                }
+                try {
+                    const files = fs.readdirSync(localDirectory).filter((entry) => !entry.startsWith('.')).length;
+                    return { relativeDir, localDirectory, readable: true, files, issues: [] };
+                }
+                catch {
+                    return { relativeDir, localDirectory, readable: false, files: 0, issues: [`Unreadable ${relativeDir}`] };
+                }
+            });
+            const readable = scanned.some((entry) => entry.readable);
+            const existing = scanned.filter((entry) => fs.existsSync(entry.localDirectory));
+            return {
+                localDirectory: existing.find((entry) => entry.relativeDir.startsWith('.agents/'))?.localDirectory
+                    ?? existing[0]?.localDirectory
+                    ?? scanned[0]?.localDirectory,
+                localDirectories: scanned.map((entry) => entry.localDirectory),
+                readable,
+                files: scanned.reduce((sum, entry) => sum + entry.files, 0),
+                issues: readable
+                    ? scanned.flatMap((entry) => entry.issues)
+                    : [`Missing ${relativeDirs.join(' or ')}`],
+            };
         };
-        const skillsDir = scanLocalDirectory('.agent/skills');
-        const workflowsDir = scanLocalDirectory('.agent/workflows');
-        const hooksDir = scanLocalDirectory('.agent/hooks');
-        const automationsDir = scanLocalDirectory('.agent/automations');
+        const skillsDir = scanLocalDirectories(['.agent/skills', '.agents/skills']);
+        const workflowsDir = scanLocalDirectories(['.agent/workflows', '.agents/workflows']);
+        const hooksDir = scanLocalDirectories(['.agent/hooks']);
+        const automationsDir = scanLocalDirectories(['.agent/automations']);
         const specialistsAvailable = this.runtime.listSpecialists().length;
         const crewsAvailable = this.runtime.listCrews().length;
         const issues = [
@@ -1444,6 +1566,7 @@ export class OrchestratorEngine {
                     rejected: Math.max(0, this.runtime.listSkills().length - selections.skills.length),
                     readable: skillsDir.readable,
                     localDirectory: skillsDir.localDirectory,
+                    localDirectories: skillsDir.localDirectories,
                     localOverrideFiles: skillsDir.files,
                     issues: skillsDir.issues,
                 },
@@ -1454,6 +1577,7 @@ export class OrchestratorEngine {
                     rejected: Math.max(0, this.runtime.listWorkflows().length - selections.workflows.length),
                     readable: workflowsDir.readable,
                     localDirectory: workflowsDir.localDirectory,
+                    localDirectories: workflowsDir.localDirectories,
                     localOverrideFiles: workflowsDir.files,
                     issues: workflowsDir.issues,
                 },
@@ -1464,6 +1588,7 @@ export class OrchestratorEngine {
                     rejected: Math.max(0, this.runtime.listHooks().length - selections.hooks.length),
                     readable: hooksDir.readable,
                     localDirectory: hooksDir.localDirectory,
+                    localDirectories: hooksDir.localDirectories,
                     localOverrideFiles: hooksDir.files,
                     issues: hooksDir.issues,
                 },
@@ -1474,6 +1599,7 @@ export class OrchestratorEngine {
                     rejected: Math.max(0, this.runtime.listAutomations().length - selections.automations.length),
                     readable: automationsDir.readable,
                     localDirectory: automationsDir.localDirectory,
+                    localDirectories: automationsDir.localDirectories,
                     localOverrideFiles: automationsDir.files,
                     issues: automationsDir.issues,
                 },
@@ -1735,7 +1861,7 @@ export class OrchestratorEngine {
                 `- **Mathematical Routing**: Applied strict TF-IDF/Vector heuristics weighted for the \`${intent.taskType}\` domain.`,
                 '',
                 '## 2. Swarm Topology (Parallel Sub-Agents)',
-                `- **Total Agents Allocated**: ${workerPlan?.workers?.length || 0}`,
+                `- **Total Agents Allocated**: ${workerPlan?.totalWorkers ?? 0}`,
                 `- **Execution Mode**: ${workerPlan?.mode || 'default'}`,
                 ...(workerPlan?.workers || []).map((w, idx) => `  - **Agent ${idx + 1}**: Uses isolated Git Worktree. Type: \`${w.type}\``),
                 '',