nexus-agents 2.79.1 → 2.79.4

package/README.md

@@ -21,7 +21,7 @@ Nexus Agents makes your AI coding tools work together intelligently. It coordina
 - **Consensus Voting** — Six aggregation strategies: simple/super-majority, unanimous, higher-order Bayesian, opinion-wise, proof-of-learning.
 - **Development Pipeline** — Research → Plan → Vote → Decompose → Implement → QA → Security. Autonomous, harness, and dry-run modes.
 - **Memory & Learning** — Multiple backends (session, belief, adaptive, routing, graph, hybrid, agentic, typed) with cross-session persistence.
-- **MCP Tools** — Agent management, workflow execution, research, memory, codebase intelligence, repo analysis, consensus, operations. See [docs/ENTRYPOINTS.md](https://github.com/williamzujkowski/nexus-agents/blob/main/docs/ENTRYPOINTS.md) for the canonical list.
+- **MCP Tools** — Agent management, workflow execution, research, memory, codebase intelligence, repo analysis, consensus, operations. See [docs/ENTRYPOINTS.md](https://github.com/nexus-substrate/nexus-agents/blob/main/docs/ENTRYPOINTS.md) for the canonical list.
 - **Research System** — Discovery across arXiv, GitHub, Semantic Scholar, and other sources with auto-catalog and synthesis.
 - **Security** — Sandboxing, trust classification, SARIF parsing, input sanitization, red team pipeline.
 
@@ -331,7 +331,7 @@ if (result.ok) {
 
 ```bash
 # Clone the repository
-git clone https://github.com/williamzujkowski/nexus-agents.git
+git clone https://github.com/nexus-substrate/nexus-agents.git
 cd nexus-agents
 
 # Install dependencies

package/dist/{child-mcp-config-CTO2MBRM.js → child-mcp-config-DFRYTRBK.js}

@@ -1,6 +1,6 @@
 import {
   createLogger
-} from "./chunk-WDYCIJWN.js";
+} from "./chunk-UQOSVOEU.js";
 import "./chunk-7BMOZJYS.js";
 import "./chunk-UP2VWCW5.js";
 
@@ -59,4 +59,4 @@ export {
   generateMcpConfig,
   getDefaultAllowedTools
 };
-//# sourceMappingURL=child-mcp-config-CTO2MBRM.js.map
+//# sourceMappingURL=child-mcp-config-DFRYTRBK.js.map

package/dist/{chunk-MGYNV3EX.js → chunk-3ENBGGYA.js}

@@ -7,10 +7,10 @@ import {
 import {
   getTokenEnvVars,
   resolveToken
-} from "./chunk-GONMG4NM.js";
+} from "./chunk-LFTK5ZQG.js";
 import {
   executeExpert
-} from "./chunk-K2QILJG4.js";
+} from "./chunk-PHBRELUK.js";
 import {
   EventTopics,
   NOOP_NOTIFIER,
@@ -36,7 +36,7 @@ import {
   withAccessPolicy,
   withProgressHeartbeat,
   wrapToolWithTimeout
-} from "./chunk-SWFJU3W2.js";
+} from "./chunk-DW3UTO43.js";
 import {
   REGISTRY_PATH,
   getProjectRoot,
@@ -45,14 +45,14 @@ import {
   normalizeTopicToCanonical,
   savePapersRegistry,
   synthesizeResearch
-} from "./chunk-5O6XLBPP.js";
+} from "./chunk-UNFS6YBY.js";
 import {
   IssueTriage,
   sanitizeInput
-} from "./chunk-6TFTVW77.js";
+} from "./chunk-BXI6DKBU.js";
 import {
   generateSecurityPlan
-} from "./chunk-FJWWSVWB.js";
+} from "./chunk-TN5ZKSGC.js";
 import {
   analyzeGitHubRepo
 } from "./chunk-7J7PNOJQ.js";
@@ -64,7 +64,7 @@ import {
   getContextForTask,
   inferTaskCategory,
   summarizeContextForPrompt
-} from "./chunk-DNO2INX5.js";
+} from "./chunk-PDCLBWH5.js";
 import {
   DEFAULT_RELEVANCE_CONFIG,
   MemoryImportance,
@@ -72,17 +72,19 @@ import {
   generateHyphenId,
   generateUUID,
   getToolMemory
-} from "./chunk-Q5CFPIJ5.js";
+} from "./chunk-NXNNT5XW.js";
 import {
   DEFAULT_TASK_TTL_MS,
   DEFAULT_TOOL_RATE_LIMITS,
-  clampTaskTtl,
+  clampTaskTtl
+} from "./chunk-UOR2JWFH.js";
+import {
   getAvailabilityCache,
   resolveFallback
-} from "./chunk-XLGI7QGQ.js";
+} from "./chunk-OFRDE7MK.js";
 import {
   DEFAULTS
-} from "./chunk-HYU4GZY6.js";
+} from "./chunk-UNRTM43V.js";
 import {
   resolveInsideRoot
 } from "./chunk-NUBSJGQZ.js";
@@ -98,7 +100,7 @@ import {
   getAvailableClis,
   sleep,
   withTimeout
-} from "./chunk-D6TM2VHX.js";
+} from "./chunk-BIH2CBC5.js";
 import {
   BUILT_IN_EXPERTS,
   BuiltInExpertTypeSchema,
@@ -110,7 +112,7 @@ import {
 } from "./chunk-PQHVC4BD.js";
 import {
   createSessionMemory
-} from "./chunk-3NIPH6UP.js";
+} from "./chunk-45NUO4FE.js";
 import {
   AGENT_ROUTER_TIMEOUTS,
   API_TIMEOUTS,
@@ -180,7 +182,7 @@ import {
   resolveModelIdentitySync,
   toExpertTaskAnalysisResult,
   withStep
-} from "./chunk-WDYCIJWN.js";
+} from "./chunk-UQOSVOEU.js";
 import {
   getNexusDataDir,
   nexusDataPath
@@ -25534,7 +25536,7 @@ function getAvailableApiKeys() {
 }
 function buildErrorMessage() {
   const keyList = API_KEYS.map((k) => `  - ${k.name} (${k.provider})`).join("\n");
-  return "No model adapter available. This operation requires either:\n\n" + CLI_AUTH_INSTRUCTIONS + "\n\n2. An API key environment variable:\n" + keyList + "\n\nSee: https://github.com/williamzujkowski/nexus-agents#prerequisites--environment";
+  return "No model adapter available. This operation requires either:\n\n" + CLI_AUTH_INSTRUCTIONS + "\n\n2. An API key environment variable:\n" + keyList + "\n\nSee: https://github.com/nexus-substrate/nexus-agents#prerequisites--environment";
 }
 async function detectAvailableClis(cache, log) {
   try {
@@ -26674,7 +26676,7 @@ async function populateUnifiedContextOnState(state) {
   try {
     const taskCandidate = state["task"];
     if (typeof taskCandidate !== "string" || taskCandidate === "") return;
-    const { getContextForTask: getContextForTask2, inferTaskCategory: inferTaskCategory2 } = await import("./context-retriever-MB3D7KS6.js");
+    const { getContextForTask: getContextForTask2, inferTaskCategory: inferTaskCategory2 } = await import("./context-retriever-6AWHCHRP.js");
     const ctx = await getContextForTask2({
       task: taskCandidate,
       category: inferTaskCategory2(taskCandidate),
@@ -41898,7 +41900,7 @@ async function tryIssueTriage(task) {
   try {
     const issueMatch = task.match(/github\.com\/([^/]+\/[^/]+)\/issues\/(\d+)/);
     if (issueMatch === null) return null;
-    const { createIssueTriage } = await import("./issue-triage-RMXPDZ2K.js");
+    const { createIssueTriage } = await import("./issue-triage-UTWKXLKC.js");
     const triage = createIssueTriage();
     const owner = issueMatch[1] ?? "";
     const num = issueMatch[2] ?? "";
@@ -41926,7 +41928,7 @@ var VALID_TEMPLATES = /* @__PURE__ */ new Set([
 ]);
 async function classifyWithLLM(task) {
   try {
-    const { executeExpert: executeExpert2 } = await import("./expert-bridge-JKLC57IC.js");
+    const { executeExpert: executeExpert2 } = await import("./expert-bridge-5YOPK5IT.js");
     const prompt = [
       "Classify this task into exactly one pipeline template.",
       "Templates: dev (implementation/bug fix/refactor), research (investigate/evaluate/compare),",
@@ -41994,7 +41996,6 @@ async function runAdaptiveOrchestrator(task, options) {
     confidence: classification.confidence
   });
   const result = await runGraphPipeline(cleanTask, template, options.stages, options);
-  recordPipelineOutcome(template.id, classification, result.success);
   return { ...result, selectionMethod, taskClassification: classification };
 }
 function resolveTemplate(templateId) {
@@ -42005,21 +42006,6 @@ function resolveTemplate(templateId) {
   if (fallback !== void 0) return fallback;
   return { id: "dev", name: "Development", stages: [] };
 }
-function recordPipelineOutcome(templateId, classification, success) {
-  try {
-    getOutcomeStore().append({
-      id: `pipeline-${templateId}-${String(Date.now())}`,
-      cli: "claude",
-      category: "code_generation",
-      model: `pipeline-${templateId}`,
-      success,
-      durationMs: 0,
-      timestamp: (/* @__PURE__ */ new Date()).toISOString(),
-      source: "delegate"
-    });
-  } catch {
-  }
-}
 
 // src/security/sarif-types.ts
 import { z as z86 } from "zod";
@@ -42695,22 +42681,30 @@ var logger37 = createLogger({ component: "agent-executor" });
 function emitStageEvent2(stage, status, details) {
   emitPipelineStageEvent("dev-pipeline", stage, status, details);
 }
-function recordOutcome(taskId, category, success, durationMs, extra) {
+function recordOutcome(args) {
+  if (args.cli === void 0) {
+    logger37.debug("Skipping outcome record \u2014 no cli (bridge failed or non-CLI stage)", {
+      taskId: args.taskId,
+      category: args.category,
+      success: args.success
+    });
+    return;
+  }
   try {
     getOutcomeStore().append({
-      id: `pipeline-${taskId}-${String(Date.now())}`,
-      cli: "claude",
-      category,
+      id: `pipeline-${args.taskId}-${String(Date.now())}`,
+      cli: args.cli,
+      category: args.category,
       model: "pipeline",
-      success,
-      durationMs,
+      success: args.success,
+      durationMs: args.durationMs,
       timestamp: (/* @__PURE__ */ new Date()).toISOString(),
       source: "delegate",
-      routingStage: extra?.routingStage,
-      retryCount: extra?.retryCount
+      routingStage: args.routingStage,
+      retryCount: args.retryCount
     });
   } catch (error) {
-    logger37.debug("Failed to record outcome", { taskId, error: String(error) });
+    logger37.debug("Failed to record outcome", { taskId: args.taskId, error: String(error) });
   }
 }
 var cachedMemory = null;
@@ -42718,7 +42712,7 @@ var memoryInitPromise = null;
 async function initPipelineMemory() {
   if (cachedMemory !== null) return cachedMemory;
   try {
-    const { createSessionMemory: createSessionMemory2 } = await import("./session-memory-L7EQIY2O.js");
+    const { createSessionMemory: createSessionMemory2 } = await import("./session-memory-XZ3NJIR4.js");
     const { getLearningDir } = await import("./learning-persistence-Q3HTOGTU.js");
     const mem = createSessionMemory2(getLearningDir());
     mem.startSession(`pipeline-${String(Date.now())}`);
@@ -42774,7 +42768,7 @@ function recordRoutingExperience(category, success, durationMs) {
     callRecord(routingMemoryCache);
     return;
   }
-  void import("./routing-memory-3B6DDZ76.js").then(({ createRoutingMemory }) => {
+  void import("./routing-memory-6DV6ZPAH.js").then(({ createRoutingMemory }) => {
     routingMemoryCache = createRoutingMemory();
     callRecord(routingMemoryCache);
   }).catch((error) => {
@@ -42803,7 +42797,7 @@ ${text}` : "";
 }
 async function getWeatherContext() {
   try {
-    const { generateWeatherReport: generateWeatherReport2 } = await import("./weather-report-ER3WUZ7S.js");
+    const { generateWeatherReport: generateWeatherReport2 } = await import("./weather-report-ZB4AKOIA.js");
     const report = generateWeatherReport2({ includeAdaptive: true });
     const mappings = "recommendedMappings" in report ? report.recommendedMappings : [];
     if (!Array.isArray(mappings) || mappings.length === 0) return "";
@@ -42821,7 +42815,7 @@ ${lines}
 }
 async function getMemoryContext(task) {
   try {
-    const { createSessionMemory: createSessionMemory2 } = await import("./session-memory-L7EQIY2O.js");
+    const { createSessionMemory: createSessionMemory2 } = await import("./session-memory-XZ3NJIR4.js");
     const { getLearningDir } = await import("./learning-persistence-Q3HTOGTU.js");
     const memory = createSessionMemory2(getLearningDir(), { maxLearningsInContext: 10 });
     const learnings = memory.searchLearnings(task.slice(0, 200));
@@ -42872,8 +42866,15 @@ ${task}`
       const combined = [discover.text, analyze.text].filter(Boolean).join("\n\n");
       const totalMs = discover.durationMs + analyze.durationMs;
       const success = discover.success || analyze.success;
+      const researchCli = discover.cli ?? analyze.cli;
       emitStageEvent2("research", success ? "completed" : "failed", { durationMs: totalMs });
-      recordOutcome("research", "research", success, totalMs);
+      recordOutcome({
+        taskId: "research",
+        category: "research",
+        cli: researchCli,
+        success,
+        durationMs: totalMs
+      });
       if (success && combined.length > 50) {
         recordLearning(
           `Research for "${task.slice(0, 80)}": ${combined.slice(0, 200)}`,
@@ -42904,7 +42905,13 @@ ${contextBlock}`;
       await postProgress(config, "Plan", feedback !== void 0 ? "Revising..." : "Planning...");
       const r = await executeExpert("architecture", prompt);
       emitStageEvent2("plan", r.success ? "completed" : "failed", { durationMs: r.durationMs });
-      recordOutcome("plan", "architecture", r.success, r.durationMs);
+      recordOutcome({
+        taskId: "plan",
+        category: "architecture",
+        cli: r.cli,
+        success: r.success,
+        durationMs: r.durationMs
+      });
       await postProgress(config, "Plan", `Done (${r.text.length} chars, ${r.durationMs}ms)`);
       return r.text || prompt;
     },
@@ -42914,7 +42921,7 @@ ${contextBlock}`;
       const strategy = config.votingStrategy ?? "higher_order";
       await postProgress(config, "Vote", `Running consensus with ${strategy} strategy...`);
       try {
-        const { executeVoting } = await import("./consensus-vote-ESFPGEJE.js");
+        const { executeVoting } = await import("./consensus-vote-CYUPIJXR.js");
         const votingResult = await executeVoting(
           {
             proposal: plan.slice(0, 4e3),
@@ -42932,7 +42939,13 @@ ${contextBlock}`;
         const feedback = votingResult.votes.filter((v) => v.vote.decision !== "approve").map((v) => v.vote.reasoning).join("\n");
         const ms = getTimeProvider().now() - start;
         emitStageEvent2("vote", "completed", { durationMs: ms });
-        recordOutcome("vote", "planning", approved, ms);
+        recordOutcome({
+          taskId: "vote",
+          category: "planning",
+          cli: void 0,
+          success: approved,
+          durationMs: ms
+        });
         await postProgress(
           config,
           "Vote",
@@ -42945,7 +42958,13 @@ ${contextBlock}`;
       } catch (error) {
         const msg = error instanceof Error ? error.message : String(error);
         emitStageEvent2("vote", "failed", { error: msg });
-        recordOutcome("vote", "planning", false, getTimeProvider().now() - start);
+        recordOutcome({
+          taskId: "vote",
+          category: "planning",
+          cli: void 0,
+          success: false,
+          durationMs: getTimeProvider().now() - start
+        });
         await postProgress(config, "Vote", `Error (auto-approved): ${msg.slice(0, 200)}`);
         return { kind: "approved", approvalPercentage: 0 };
       }
@@ -42962,7 +42981,13 @@ ${plan}`
       );
       const tasks = parseTasksFromResponse(r.text, plan);
       emitStageEvent2("decompose", "completed", { durationMs: r.durationMs });
-      recordOutcome("decompose", "planning", r.success, r.durationMs);
+      recordOutcome({
+        taskId: "decompose",
+        category: "planning",
+        cli: r.cli,
+        success: r.success,
+        durationMs: r.durationMs
+      });
       await postProgress(config, "PM", `${tasks.length} task(s)`);
       return tasks;
     },
@@ -42982,7 +43007,13 @@ ${task.description}${fb}`
       emitStageEvent2(`impl-${task.id}`, r.success ? "completed" : "failed", {
         durationMs: r.durationMs
       });
-      recordOutcome(task.id, "code_generation", r.success, r.durationMs);
+      recordOutcome({
+        taskId: task.id,
+        category: "code_generation",
+        cli: r.cli,
+        success: r.success,
+        durationMs: r.durationMs
+      });
       recordRoutingExperience("code_generation", r.success, r.durationMs);
       await postProgress(config, `Code [${task.id}]`, `Done (${r.durationMs}ms)`);
       return r.text || `[Implementation failed: ${r.error}]`;
@@ -43005,7 +43036,13 @@ Verdict: PASS/NEEDS_WORK/REJECT`
       emitStageEvent2(`qa-${task.id}`, review.verdict === "pass" ? "completed" : "failed", {
         durationMs: r.durationMs
       });
-      recordOutcome(task.id, "code_review", review.verdict === "pass", r.durationMs);
+      recordOutcome({
+        taskId: task.id,
+        category: "code_review",
+        cli: r.cli,
+        success: review.verdict === "pass",
+        durationMs: r.durationMs
+      });
       if (review.verdict === "pass") {
         recordLearning(`Task "${task.title}" passed QA`, 0.8, "pipeline-qa");
       } else {
@@ -43027,7 +43064,13 @@ Verdict: PASS/NEEDS_WORK/REJECT`
       const passed = result.verdict !== "fail";
       const ms = getTimeProvider().now() - start;
       emitStageEvent2("security", passed ? "completed" : "failed", { durationMs: ms });
-      recordOutcome("security", "security_review", passed, ms);
+      recordOutcome({
+        taskId: "security",
+        category: "security_review",
+        cli: void 0,
+        success: passed,
+        durationMs: ms
+      });
       await postProgress(config, "Security", passed ? "Passed" : `BLOCKED: ${result.details}`);
       flushPipelineMemory();
       return { passed, feedback: result.details };
@@ -43772,7 +43815,7 @@ async function extractSymbolsForTask(task) {
 }
 async function queryResearchRegistry(task) {
   try {
-    const { synthesizeResearch: synthesizeResearch2 } = await import("./research-helpers-synthesize-K2UCJQQG.js");
+    const { synthesizeResearch: synthesizeResearch2 } = await import("./research-helpers-synthesize-77TLYSW4.js");
     const topic = task.split(/[.!?\n]/).filter((s) => s.trim().length > 10)[0]?.trim();
     if (topic === void 0) return null;
     const result = await synthesizeResearch2(topic.slice(0, 50));
@@ -43857,7 +43900,7 @@ function createScanStageWrapper() {
       try {
         const slug = ctx.task.match(/([a-zA-Z0-9._-]+\/[a-zA-Z0-9._-]+)/)?.[1];
         if (slug !== void 0) {
-          const { generateSecurityPlan: generateSecurityPlan2 } = await import("./repo-security-plan-AGRU72DL.js");
+          const { generateSecurityPlan: generateSecurityPlan2 } = await import("./repo-security-plan-HNLMF7J7.js");
           const plan = await generateSecurityPlan2({ repo: slug, maxScanners: 10 });
           const recs = plan.recommendations.slice(0, 5).map((r) => `${r.priority}: ${r.displayName} (${r.category})`).join("; ");
           ctx.sharedMemory.write("scan", "decision", { recommendations: recs });
@@ -49260,7 +49303,7 @@ function createDeprecatedModeFallback(requestedMode, policyConfig) {
   logger46.warn(`Sandbox mode "${requestedMode}" is no longer supported; using "policy" mode`, {
     requestedMode,
     actualMode: "policy",
-    reason: "In-process Docker/Deno executors were deleted in #2551. Use the OpenCode sandbox bootstrap for real isolation (NEXUS_SANDBOX environment variable, see docs/getting-started/SANDBOXED-USAGE.md)."
+    reason: "In-process Docker/Deno executors were deleted in #2551. Use the OpenCode sandbox bootstrap for real isolation (NEXUS_SANDBOX environment variable, see docs/guides/SANDBOXED-USAGE.md)."
   });
   const executor = new PolicySandboxExecutor(policyConfig);
   return {
@@ -49424,7 +49467,7 @@ var GitHubTaskTracker = class {
   cachedProvider = null;
   async getProvider() {
     if (this.cachedProvider !== null) return this.cachedProvider;
-    const { createScmProvider } = await import("./factory-BUUXNGIB.js");
+    const { createScmProvider } = await import("./factory-DN7SJZ5Z.js");
     const result = await createScmProvider({ repo: this.config.repo ?? "" });
     if (!result.ok) throw new Error(`SCM provider error: ${result.error.message}`);
     this.cachedProvider = result.value;
@@ -50129,4 +50172,4 @@ export {
   detectBackend,
   createTaskTracker
 };
-//# sourceMappingURL=chunk-MGYNV3EX.js.map
+//# sourceMappingURL=chunk-3ENBGGYA.js.map