agentic-qe 3.9.14 → 3.9.16

package/dist/cli/chunks/{windsurf-installer-2SGRCS6C.js → windsurf-installer-RVCDSJT3.js}

@@ -1,5 +1,5 @@
-import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.14");process.exit(0)}
-import{b as u}from"./chunk-AOYN6XYJ.js";import{a as f,c as h}from"./chunk-UIYK4Y7K.js";import"./chunk-DGUAAG3T.js";h();import{existsSync as i,mkdirSync as d,readFileSync as g,writeFileSync as a}from"fs";import{join as p,dirname as v}from"path";var c=class{projectRoot;overwrite;generator;constructor(e){this.projectRoot=e.projectRoot,this.overwrite=e.overwrite??!1,this.generator=u()}async install(){let e={success:!0,mcpConfigured:!1,rulesInstalled:!1,errors:[],configPath:"",rulesPath:""};try{let t=this.generator.generateMcpConfig("windsurf"),r=p(this.projectRoot,t.path);if(e.configPath=r,!i(r)||this.overwrite){let o=v(r);if(i(o)||d(o,{recursive:!0}),i(r)&&this.overwrite){let m=this.mergeExistingConfig(r,t.content);a(r,m)}else a(r,t.content);e.mcpConfigured=!0}let n=this.generator.generateBehavioralRules("windsurf"),s=p(this.projectRoot,n.path);if(e.rulesPath=s,!i(s)||this.overwrite){if(i(s)&&this.overwrite){let o=this.mergeExistingRules(s,n.content);a(s,o)}else a(s,n.content);e.rulesInstalled=!0}}catch(t){e.success=!1,e.errors.push(`Windsurf installation failed: ${f(t)}`)}return e}mergeExistingConfig(e,t){try{let r=JSON.parse(g(e,"utf-8")),n=JSON.parse(t);return r.mcpServers||(r.mcpServers={}),Object.assign(r.mcpServers,n.mcpServers),JSON.stringify(r,null,2)+`
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import{b as u}from"./chunk-HFGCLV56.js";import{a as f,c as h}from"./chunk-V2ELGHLG.js";import"./chunk-NOJVROCD.js";h();import{existsSync as i,mkdirSync as d,readFileSync as g,writeFileSync as a}from"fs";import{join as p,dirname as v}from"path";var c=class{projectRoot;overwrite;generator;constructor(e){this.projectRoot=e.projectRoot,this.overwrite=e.overwrite??!1,this.generator=u()}async install(){let e={success:!0,mcpConfigured:!1,rulesInstalled:!1,errors:[],configPath:"",rulesPath:""};try{let t=this.generator.generateMcpConfig("windsurf"),r=p(this.projectRoot,t.path);if(e.configPath=r,!i(r)||this.overwrite){let o=v(r);if(i(o)||d(o,{recursive:!0}),i(r)&&this.overwrite){let m=this.mergeExistingConfig(r,t.content);a(r,m)}else a(r,t.content);e.mcpConfigured=!0}let n=this.generator.generateBehavioralRules("windsurf"),s=p(this.projectRoot,n.path);if(e.rulesPath=s,!i(s)||this.overwrite){if(i(s)&&this.overwrite){let o=this.mergeExistingRules(s,n.content);a(s,o)}else a(s,n.content);e.rulesInstalled=!0}}catch(t){e.success=!1,e.errors.push(`Windsurf installation failed: ${f(t)}`)}return e}mergeExistingConfig(e,t){try{let r=JSON.parse(g(e,"utf-8")),n=JSON.parse(t);return r.mcpServers||(r.mcpServers={}),Object.assign(r.mcpServers,n.mcpServers),JSON.stringify(r,null,2)+`
 `}catch{return t}}mergeExistingRules(e,t){try{let r=g(e,"utf-8");return r.includes("Agentic QE")||r.includes("fleet_init")?r:r.trimEnd()+`
 
 ---

package/dist/cli/chunks/witness-chain-5R322YYF.js

@@ -0,0 +1,2 @@
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import{a,b,c,d,e,f,g,h}from"./chunk-CR7LLS26.js";import"./chunk-H4BZJVKU.js";import"./chunk-TWEBJWJI.js";import"./chunk-5LDXAVDC.js";import"./chunk-KR7S4IZZ.js";import"./chunk-4PFHQH4B.js";import"./chunk-V2ELGHLG.js";import"./chunk-RFLSJ7OL.js";import"./chunk-T7VIUEKI.js";import"./chunk-3CAPNE2H.js";import"./chunk-77OVXVN2.js";import"./chunk-MJKFU6A6.js";import"./chunk-HJUC2DE6.js";import"./chunk-GB6D3SSY.js";import"./chunk-NIXMFJJC.js";import"./chunk-W6TMZY5R.js";import"./chunk-NOJVROCD.js";export{a as GENESIS_PREV_HASH,f as WitnessChain,h as createWitnessChain,g as getWitnessChain,d as hashWith,e as serializeEntry,b as sha256,c as shake256};

package/dist/cli/chunks/{witness-chain-LJUYOCB5.js → witness-chain-YDFB22MT.js}

@@ -1,2 +1,2 @@
-import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.14");process.exit(0)}
-import{a,b,c,d,e,f,g}from"./chunk-4RDTR2OF.js";import"./chunk-STYNOKOM.js";import"./chunk-GUEK5DOK.js";import"./chunk-5HUAD4UU.js";import"./chunk-DGUAAG3T.js";export{c as PersistentWitnessChain,a as SPRTAccumulator,b as WitnessChain,f as createPersistentWitnessChain,e as createWitnessChain,d as createWitnessChainSQLitePersistence,g as isWitnessChainFeatureEnabled};
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import{a,b,c,d,e,f,g}from"./chunk-T36IXY5W.js";import"./chunk-5LDXAVDC.js";import"./chunk-KR7S4IZZ.js";import"./chunk-W6TMZY5R.js";import"./chunk-NOJVROCD.js";export{c as PersistentWitnessChain,a as SPRTAccumulator,b as WitnessChain,f as createPersistentWitnessChain,e as createWitnessChain,d as createWitnessChainSQLitePersistence,g as isWitnessChainFeatureEnabled};

package/dist/cli/chunks/{workflow-QORI3KO7.js → workflow-MHW4KHNK.js}

@@ -1,5 +1,5 @@
-import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.14");process.exit(0)}
-import"./chunk-I5U64MHU.js";import{b as $}from"./chunk-OGLS6HB4.js";import{d as R}from"./chunk-VEAVDXXT.js";import{b as k,c as C,d as b}from"./chunk-OZBTC26R.js";import{c as W}from"./chunk-DMZ2XOEW.js";import"./chunk-PZF5ISGS.js";import"./chunk-UIYK4Y7K.js";import"./chunk-DGUAAG3T.js";import{Command as O}from"commander";import o from"chalk";function P(d,a){let m=d.indexOf("=");return m>0&&(a[d.substring(0,m)]=d.substring(m+1)),a}function x(d,a,m){let y=new O("workflow").description("Manage QE workflows and pipelines (ADR-041)");return y.command("run <file>").description("Execute a QE pipeline from YAML file").option("-w, --watch","Watch execution progress").option("-v, --verbose","Show detailed output").option("--params <json>","Additional parameters as JSON","{}").action(async(t,l)=>{if(!await m())return;let e=await import("fs"),c=(await import("path")).resolve(t);try{console.log(o.blue(`
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import"./chunk-7DP2IQ6F.js";import{b as $}from"./chunk-DJPS7H2M.js";import{d as R}from"./chunk-SMNOZEM7.js";import{b as k,c as C,d as b}from"./chunk-3K4IX7L4.js";import{c as W}from"./chunk-4PFHQH4B.js";import"./chunk-EFTK4ZVP.js";import"./chunk-V2ELGHLG.js";import"./chunk-NOJVROCD.js";import{Command as O}from"commander";import o from"chalk";function P(d,a){let m=d.indexOf("=");return m>0&&(a[d.substring(0,m)]=d.substring(m+1)),a}function x(d,a,m){let y=new O("workflow").description("Manage QE workflows and pipelines (ADR-041)");return y.command("run <file>").description("Execute a QE pipeline from YAML file").option("-w, --watch","Watch execution progress").option("-v, --verbose","Show detailed output").option("--params <json>","Additional parameters as JSON","{}").action(async(t,l)=>{if(!await m())return;let e=await import("fs"),c=(await import("path")).resolve(t);try{console.log(o.blue(`
  Running workflow from: ${t}
 `));let s=k(c);if(!s.success||!s.workflow){console.log(o.red("Failed to parse pipeline:"));for(let w of s.errors)console.log(o.red(`   ${w}`));await a(1)}let r={...W(l.params,"params")};if(s.pipeline){for(let w of s.pipeline.stages)if(w.params)for(let[S,h]of Object.entries(w.params))r[S]=h}if(!d.workflowOrchestrator.getWorkflow(s.workflow.id)){let w=d.workflowOrchestrator.registerWorkflow(s.workflow);w.success||(console.log(o.red(`Failed to register workflow: ${w.error.message}`)),await a(1))}let n=await d.workflowOrchestrator.executeWorkflow(s.workflow.id,r);if(!n.success){console.log(o.red(`Failed to start workflow: ${n.error.message}`)),await a(1);return}let p=n.value;if(console.log(o.cyan(`  Execution ID: ${p}`)),console.log(o.gray(`  Workflow: ${s.workflow.name}`)),console.log(o.gray(`  Stages: ${s.workflow.steps.length}`)),console.log(""),l.watch){console.log(o.blue(`Workflow Progress:
 `));let w,S=Date.now();for(;;){let g=d.workflowOrchestrator.getWorkflowStatus(p);if(!g)break;if(!w||w.progress!==g.progress||w.status!==g.status||JSON.stringify(w.currentSteps)!==JSON.stringify(g.currentSteps)){process.stdout.write("\r\x1B[K");let v="\u2588".repeat(Math.floor(g.progress/5))+"\u2591".repeat(20-Math.floor(g.progress/5)),D=g.status==="completed"?o.green:g.status==="failed"?o.red:g.status==="running"?o.yellow:o.gray;console.log(`  [${v}] ${g.progress}% - ${D(g.status)}`),g.currentSteps.length>0&&l.verbose&&console.log(o.gray(`    Running: ${g.currentSteps.join(", ")}`)),w=g}if(g.status==="completed"||g.status==="failed"||g.status==="cancelled")break;await new Promise(v=>setTimeout(v,500))}let h=d.workflowOrchestrator.getWorkflowStatus(p);if(h){console.log("");let g=h.duration||Date.now()-S;h.status==="completed"?(console.log(o.green("Workflow completed successfully")),console.log(o.gray(`   Duration: ${$(g)}`)),console.log(o.gray(`   Completed: ${h.completedSteps.length} stages`)),h.skippedSteps.length>0&&console.log(o.yellow(`   Skipped: ${h.skippedSteps.length} stages`))):h.status==="failed"?(console.log(o.red("Workflow failed")),console.log(o.red(`   Error: ${h.error}`)),console.log(o.gray(`   Failed stages: ${h.failedSteps.join(", ")}`))):console.log(o.yellow(`Workflow ${h.status}`))}}else console.log(o.green("Workflow execution started")),console.log(o.gray(`   Use 'aqe workflow status ${p}' to check progress`));console.log(""),await a(0)}catch(s){console.error(o.red(`
@@ -35,10 +35,10 @@ Workflow cancelled: ${t}
 `)):console.log(o.red(`
 Failed to cancel workflow: ${l.error.message}
 `)),await a(l.success?0:1)}catch(l){console.error(o.red(`
-Failed to cancel workflow:`),l),await a(1)}}),y.command("browser-list").description("List available browser workflow templates").action(async()=>{try{let{BrowserWorkflowTool:t}=await import("./browser-workflow-CSARLAJD.js"),e=await new t().invoke({});if(e.success&&e.data){console.log(o.blue(`
+Failed to cancel workflow:`),l),await a(1)}}),y.command("browser-list").description("List available browser workflow templates").action(async()=>{try{let{BrowserWorkflowTool:t}=await import("./browser-workflow-KVHPOIBA.js"),e=await new t().invoke({});if(e.success&&e.data){console.log(o.blue(`
  Browser Workflow Templates:
 `));for(let u of e.data.availableTemplates)console.log(`  ${o.cyan(u)}`);console.log("")}else console.log(o.red(`Failed: ${e.error||"Unknown error"}`));await a(0)}catch(t){console.error(o.red(`
-Failed:`),t),await a(1)}}),y.command("browser-load [template]").description("Load and validate a browser workflow template or inline YAML").option("--yaml <yaml>","Inline YAML workflow definition").option("-v, --var <key=value>","Variable override (repeatable)",P,{}).option("-F, --format <format>","Output format (text|json)","text").option("-o, --output <path>","Write output to file").action(async(t,l)=>{try{let{BrowserWorkflowTool:e}=await import("./browser-workflow-CSARLAJD.js"),{writeOutput:u,toJSON:c}=await import("./ci-output-QC4WRENA.js"),s=new e,f={variables:l.var||{}};if(l.yaml)f.workflowYaml=l.yaml;else if(t)if(t.endsWith(".yaml")||t.endsWith(".yml")){let i=await import("fs"),p=(await import("path")).resolve(t);i.existsSync(p)||(console.log(o.red(`
+Failed:`),t),await a(1)}}),y.command("browser-load [template]").description("Load and validate a browser workflow template or inline YAML").option("--yaml <yaml>","Inline YAML workflow definition").option("-v, --var <key=value>","Variable override (repeatable)",P,{}).option("-F, --format <format>","Output format (text|json)","text").option("-o, --output <path>","Write output to file").action(async(t,l)=>{try{let{BrowserWorkflowTool:e}=await import("./browser-workflow-KVHPOIBA.js"),{writeOutput:u,toJSON:c}=await import("./ci-output-TKESU45X.js"),s=new e,f={variables:l.var||{}};if(l.yaml)f.workflowYaml=l.yaml;else if(t)if(t.endsWith(".yaml")||t.endsWith(".yml")){let i=await import("fs"),p=(await import("path")).resolve(t);i.existsSync(p)||(console.log(o.red(`
 File not found: ${p}
 `)),await a(1)),f.workflowYaml=i.readFileSync(p,"utf-8")}else f.templateName=t;else console.log(o.red(`
 Provide a template name or --yaml. Use "workflow browser-list" to see templates.

package/dist/cli/chunks/workflow-orchestrator-637BCZI4.js

@@ -0,0 +1,2 @@
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import{a,b,c,d}from"./chunk-OP7X434R.js";import"./chunk-7JFSMXIA.js";import"./chunk-H4BZJVKU.js";import"./chunk-TWEBJWJI.js";import"./chunk-5LDXAVDC.js";import"./chunk-KR7S4IZZ.js";import"./chunk-4PFHQH4B.js";import"./chunk-EFTK4ZVP.js";import"./chunk-V2ELGHLG.js";import"./chunk-ED5OUSYZ.js";import"./chunk-RFLSJ7OL.js";import"./chunk-T7VIUEKI.js";import"./chunk-3CAPNE2H.js";import"./chunk-77OVXVN2.js";import"./chunk-MJKFU6A6.js";import"./chunk-HJUC2DE6.js";import"./chunk-GB6D3SSY.js";import"./chunk-NIXMFJJC.js";import"./chunk-W6TMZY5R.js";import"./chunk-NOJVROCD.js";export{b as DEFAULT_WORKFLOW_CONFIG,a as WorkflowEvents,c as WorkflowOrchestrator,d as createWorkflowOrchestrator};

package/dist/cli/chunks/{wrappers-3NR7LNB5.js → wrappers-SAZY3C2S.js}

@@ -1,2 +1,2 @@
-import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.14");process.exit(0)}
-import{a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v as L,w as M,x as N}from"./chunk-5MWNXDQW.js";import"./chunk-ZFZX2NA3.js";import"./chunk-UUVTLYUK.js";import"./chunk-STYNOKOM.js";import"./chunk-GUEK5DOK.js";import{a as v,b as w,c as x,d as y,e as z,f as A,g as B,h as C,i as D,j as E,k as F,l as G,m as H,n as I,o as J,p as K}from"./chunk-VU4QET3C.js";import"./chunk-DMZ2XOEW.js";import"./chunk-UIYK4Y7K.js";import"./chunk-LWHM5BWD.js";import"./chunk-J3XLOHWB.js";import"./chunk-JN7MSUGK.js";import"./chunk-JNLKLC7G.js";import"./chunk-WE7KIXR6.js";import"./chunk-XNXOW7BQ.js";import"./chunk-JLBUS4PR.js";import"./chunk-DJLRRCR6.js";import"./chunk-5HUAD4UU.js";import"./chunk-DGUAAG3T.js";export{z as GNNLayerFactory,i as QEFlashAttention,x as QEGNNEmbeddingIndex,y as QEGNNIndexFactory,a as QESONA,e as QE_FLASH_ATTENTION_CONFIG,g as QE_PERFORMANCE_TARGETS,f as QE_SONA_CONFIG,A as TensorCompressionFactory,u as batchComputeAttention,K as batchDifferentiableSearch,M as checkRuvectorPackagesAvailable,c as createDomainQESONA,j as createQEFlashAttention,b as createQESONA,D as getDifferentiableSearch,F as getGetCompressionLevel,E as getHierarchicalForward,G as getInit,h as getOptimalBlockConfig,k as getQEFlashAttentionConfig,n as getRuvectorDotProductAttention,m as getRuvectorFlashAttention,p as getRuvectorHyperbolicAttention,B as getRuvectorLayer,q as getRuvectorLinearAttention,r as getRuvectorMoEAttention,o as getRuvectorMultiHeadAttention,L as getRuvectorPackageVersions,C as getTensorCompress,l as getWorkloadTypes,N as initAllRuvectorPackages,w as initGNN,d as isAttentionAvailable,v as isGNNAvailable,s as toFloat32Array,H as toFloat32ArrayGNN,J as toIEmbedding,t as toNumberArrayAttn,I as toNumberArrayGNN};
+import{createRequire as __cr}from"module";const require=__cr(import.meta.url);if(process.argv.includes('--version')||process.argv.includes('-v')){console.log("3.9.16");process.exit(0)}
+import{a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v as L,w as M,x as N}from"./chunk-HXF4FUPY.js";import"./chunk-H4BZJVKU.js";import"./chunk-TWEBJWJI.js";import"./chunk-5LDXAVDC.js";import"./chunk-KR7S4IZZ.js";import{a as v,b as w,c as x,d as y,e as z,f as A,g as B,h as C,i as D,j as E,k as F,l as G,m as H,n as I,o as J,p as K}from"./chunk-7MF6LVLH.js";import"./chunk-4PFHQH4B.js";import"./chunk-V2ELGHLG.js";import"./chunk-RFLSJ7OL.js";import"./chunk-T7VIUEKI.js";import"./chunk-3CAPNE2H.js";import"./chunk-77OVXVN2.js";import"./chunk-MJKFU6A6.js";import"./chunk-HJUC2DE6.js";import"./chunk-GB6D3SSY.js";import"./chunk-NIXMFJJC.js";import"./chunk-W6TMZY5R.js";import"./chunk-NOJVROCD.js";export{z as GNNLayerFactory,i as QEFlashAttention,x as QEGNNEmbeddingIndex,y as QEGNNIndexFactory,a as QESONA,e as QE_FLASH_ATTENTION_CONFIG,g as QE_PERFORMANCE_TARGETS,f as QE_SONA_CONFIG,A as TensorCompressionFactory,u as batchComputeAttention,K as batchDifferentiableSearch,M as checkRuvectorPackagesAvailable,c as createDomainQESONA,j as createQEFlashAttention,b as createQESONA,D as getDifferentiableSearch,F as getGetCompressionLevel,E as getHierarchicalForward,G as getInit,h as getOptimalBlockConfig,k as getQEFlashAttentionConfig,n as getRuvectorDotProductAttention,m as getRuvectorFlashAttention,p as getRuvectorHyperbolicAttention,B as getRuvectorLayer,q as getRuvectorLinearAttention,r as getRuvectorMoEAttention,o as getRuvectorMultiHeadAttention,L as getRuvectorPackageVersions,C as getTensorCompress,l as getWorkloadTypes,N as initAllRuvectorPackages,w as initGNN,d as isAttentionAvailable,v as isGNNAvailable,s as toFloat32Array,H as toFloat32ArrayGNN,J as toIEmbedding,t as toNumberArrayAttn,I as toNumberArrayGNN};

package/dist/cli/commands/eval.js

@@ -14,7 +14,9 @@ import { Command } from 'commander';
 import chalk from 'chalk';
 import * as fs from 'fs';
 import * as path from 'path';
+import * as yaml from 'yaml';
 import { createParallelEvalRunner, DEFAULT_PARALLEL_EVAL_CONFIG, } from '../../validation/parallel-eval-runner.js';
+import { createCommandEvalRunner, isCommandEvalSuite, } from '../../validation/command-eval-runner.js';
 import { createSkillValidationLearner, } from '../../learning/skill-validation-learner.js';
 import { createRealQEReasoningBank, } from '../../learning/real-qe-reasoning-bank.js';
 // ============================================================================
@@ -185,6 +187,70 @@ function formatMarkdownReport(results) {
     return lines.join('\n');
 }
 // ============================================================================
+// Suite-shape dispatch
+// ============================================================================
+const DEFAULT_SKILLS_DIR = '.claude/skills';
+/**
+ * Peek at the eval yaml to decide whether the suite is command-mode
+ * (scripts producing JSON, per ADR-091) or LLM-mode (prompts evaluated by
+ * an LLM, the pre-existing shape). Returns null if the file is missing or
+ * unparseable; that error path is then surfaced by the respective runner.
+ */
+function detectSuiteMode(skill) {
+    const evalPath = path.join(process.cwd(), DEFAULT_SKILLS_DIR, skill, 'evals', `${skill}.yaml`);
+    if (!fs.existsSync(evalPath))
+        return null;
+    try {
+        const raw = yaml.parse(fs.readFileSync(evalPath, 'utf-8'));
+        return isCommandEvalSuite(raw) ? 'command' : 'llm';
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Adapt a {@link CommandEvalResult} into the {@link ParallelEvalResult} shape
+ * so the existing CLI formatting / reporting path works unchanged. Fields
+ * that don't apply to shell-command evals (model, reasoning quality,
+ * parallel speedup, worker count) are filled with sensible neutral values.
+ */
+function commandResultToParallel(cr, model) {
+    return {
+        skill: cr.skill,
+        model,
+        totalTests: cr.totalTests,
+        passedTests: cr.passedTests,
+        failedTests: cr.failedTests,
+        skippedTests: 0,
+        passRate: cr.passRate,
+        testResults: cr.testResults.map((t) => toParallelTestResult(t)),
+        totalDurationMs: cr.totalDurationMs,
+        parallelSpeedup: 1,
+        avgReasoningQuality: 0,
+        passed: cr.passed,
+        workersUsed: 1,
+        timestamp: cr.timestamp,
+    };
+}
+function toParallelTestResult(t) {
+    const errorParts = [];
+    if (t.setupFailure)
+        errorParts.push(t.setupFailure);
+    if (t.failures.length)
+        errorParts.push(...t.failures);
+    return {
+        testId: t.testId,
+        passed: t.passed,
+        expectedPatterns: [],
+        actualPatterns: [],
+        reasoningQuality: 0,
+        executionTimeMs: t.durationMs,
+        category: t.category ?? 'uncategorized',
+        priority: (t.priority ?? 'medium'),
+        error: errorParts.length ? errorParts.join('; ') : undefined,
+    };
+}
+// ============================================================================
 // Command Handlers
 // ============================================================================
 async function initializeRunner() {
@@ -209,6 +275,26 @@ async function initializeRunner() {
 async function handleRunCommand(options) {
     console.log(chalk.bold('\nAQE Parallel Eval Runner'));
     console.log(chalk.dim('ADR-056 Phase 5: Worker Pool Pattern\n'));
+    const suiteMode = detectSuiteMode(options.skill);
+    if (suiteMode === 'command') {
+        // Command-mode skills (e.g. qe-browser) don't need an LLM executor or a
+        // ReasoningBank. Keep them on a fast, dependency-light path.
+        console.log(chalk.cyan(`Running eval suite: ${options.skill}`));
+        console.log(chalk.dim('Mode: command-eval (shell-based, ADR-091)'));
+        console.log('');
+        const commandRunner = createCommandEvalRunner({
+            timeoutMs: options.timeout,
+        });
+        const commandResult = await commandRunner.run(options.skill);
+        const result = commandResultToParallel(commandResult, options.model);
+        console.log(formatResult(result));
+        if (options.output) {
+            const outputPath = path.resolve(options.output);
+            fs.writeFileSync(outputPath, JSON.stringify(result, null, 2));
+            console.log(chalk.green(`Results saved to: ${outputPath}`));
+        }
+        process.exit(result.passed ? 0 : 1);
+    }
     const { runner, reasoningBank } = await initializeRunner();
     try {
         // Configure runner

package/dist/cli/commands/upgrade.d.ts

@@ -0,0 +1,96 @@
+/**
+ * `aqe upgrade` — read-only advisory
+ *
+ * Detects which optional native bindings load on this platform and prints a
+ * report with recommendations. Does NOT modify feature flags, env vars, or
+ * config files — it only tells the user what they'd gain by installing the
+ * missing optional deps.
+ *
+ * Related: issue #383 item 2.
+ */
+import { Command } from 'commander';
+export type LoadStatus = 'loaded' | 'missing' | 'required-missing';
+export interface NativeCheck {
+    /** npm package name as it appears in package.json */
+    readonly packageName: string;
+    /** Human-readable role */
+    readonly role: string;
+    /** What the fallback looks like when missing (not applicable for required deps) */
+    readonly fallback: string;
+    /** Feature flag(s) this native affects (informational) */
+    readonly affectsFlags: readonly string[];
+    /** Whether missing is fatal or just degrades performance */
+    readonly required: boolean;
+}
+export interface NativeResult extends NativeCheck {
+    readonly status: LoadStatus;
+    /** Error message if the load failed (missing means MODULE_NOT_FOUND; other errors get surfaced). */
+    readonly loadError?: string;
+}
+export interface EnvOverride {
+    readonly envVar: string;
+    readonly value: string;
+    readonly flagName: string;
+}
+export interface Recommendation {
+    readonly severity: 'info' | 'warn' | 'error';
+    readonly message: string;
+    /** Copy-paste install command, when relevant. */
+    readonly action?: string;
+}
+export interface UpgradeReport {
+    readonly aqeVersion: string;
+    readonly platform: {
+        readonly os: string;
+        readonly arch: string;
+        readonly node: string;
+    };
+    readonly natives: readonly NativeResult[];
+    readonly flags: {
+        readonly useRVFPatternStore: boolean;
+        readonly useSublinearSolver: boolean;
+        readonly useNativeHNSW: boolean;
+        readonly useGraphMAEEmbeddings: boolean;
+        readonly useQEFlashAttention: boolean;
+    };
+    readonly envOverrides: readonly EnvOverride[];
+    readonly recommendations: readonly Recommendation[];
+    readonly summary: {
+        readonly requiredOk: boolean;
+        readonly optionalMissingCount: number;
+        readonly optionalLoadedCount: number;
+    };
+}
+/**
+ * The set of packages `aqe upgrade` inspects. Order controls the report
+ * rendering order.
+ */
+export declare const NATIVE_CATALOG: readonly NativeCheck[];
+export type LoadProbe = (packageName: string) => {
+    ok: true;
+} | {
+    ok: false;
+    error: Error;
+};
+/** Default probe — uses a CJS require relative to this module's location. */
+export declare function createDefaultLoadProbe(): LoadProbe;
+export declare function detectNatives(catalog: readonly NativeCheck[], probe: LoadProbe): NativeResult[];
+export declare function readEnvOverrides(env: NodeJS.ProcessEnv): EnvOverride[];
+interface RecommendationInput {
+    readonly natives: readonly NativeResult[];
+    readonly flags: UpgradeReport['flags'];
+    readonly envOverrides: readonly EnvOverride[];
+}
+export declare function buildRecommendations(input: RecommendationInput): Recommendation[];
+export interface BuildReportInput {
+    readonly aqeVersion: string;
+    readonly probe: LoadProbe;
+    readonly env: NodeJS.ProcessEnv;
+    readonly flags: UpgradeReport['flags'];
+}
+export declare function buildReport(input: BuildReportInput): UpgradeReport;
+export declare function exitCodeFor(report: UpgradeReport, strict: boolean): number;
+export declare function renderReportHuman(report: UpgradeReport): string;
+export declare function createUpgradeCommand(cleanupAndExit: (code: number) => Promise<never>): Command;
+export {};
+//# sourceMappingURL=upgrade.d.ts.map

package/dist/cli/commands/upgrade.js

@@ -0,0 +1,342 @@
+/**
+ * `aqe upgrade` — read-only advisory
+ *
+ * Detects which optional native bindings load on this platform and prints a
+ * report with recommendations. Does NOT modify feature flags, env vars, or
+ * config files — it only tells the user what they'd gain by installing the
+ * missing optional deps.
+ *
+ * Related: issue #383 item 2.
+ */
+import { Command } from 'commander';
+import chalk from 'chalk';
+import { createRequire } from 'node:module';
+import { platform, arch } from 'node:os';
+import { getRuVectorFeatureFlags } from '../../integrations/ruvector/feature-flags.js';
+// ============================================================================
+// Native catalog
+// ============================================================================
+/**
+ * The set of packages `aqe upgrade` inspects. Order controls the report
+ * rendering order.
+ */
+export const NATIVE_CATALOG = [
+    {
+        packageName: 'better-sqlite3',
+        role: 'SQLite storage (required — memory.db, patterns, audit)',
+        fallback: 'n/a — required',
+        affectsFlags: [],
+        required: true,
+    },
+    {
+        packageName: 'web-tree-sitter',
+        role: 'Tree-sitter WASM parser runtime (required — code intelligence)',
+        fallback: 'n/a — required',
+        affectsFlags: [],
+        required: true,
+    },
+    {
+        packageName: 'hnswlib-node',
+        role: 'Canonical HNSW vector index (default since ADR-090)',
+        fallback: 'ProgressiveHnswBackend (JS) — correct but slower on large codebases',
+        affectsFlags: ['useNativeHNSW'],
+        required: false,
+    },
+    {
+        packageName: '@ruvector/rvf-node',
+        role: 'Persistent HNSW pattern store + RVF brain export format',
+        fallback: 'SQLite-backed HNSW + JSONL brain export',
+        affectsFlags: ['useRVFPatternStore'],
+        required: false,
+    },
+    {
+        packageName: '@ruvector/solver-node',
+        role: 'Sublinear PageRank on the pattern citation graph',
+        fallback: 'TypeScript power iteration — O(n·m) (practical cap ≈ 50K nodes)',
+        affectsFlags: ['useSublinearSolver'],
+        required: false,
+    },
+    {
+        packageName: '@ruvector/attention',
+        role: 'Flash Attention with SIMD acceleration',
+        fallback: 'Plain attention — 2.5–7× slower on large sequences',
+        affectsFlags: ['useQEFlashAttention'],
+        required: false,
+    },
+    {
+        packageName: '@ruvector/gnn',
+        role: 'GraphMAE native acceleration',
+        fallback: 'TypeScript GraphMAE — correct but slower',
+        affectsFlags: ['useGraphMAEEmbeddings'],
+        required: false,
+    },
+];
+/** Default probe — uses a CJS require relative to this module's location. */
+export function createDefaultLoadProbe() {
+    const req = createRequire(import.meta.url);
+    return (packageName) => {
+        try {
+            req(packageName);
+            return { ok: true };
+        }
+        catch (err) {
+            return { ok: false, error: err instanceof Error ? err : new Error(String(err)) };
+        }
+    };
+}
+export function detectNatives(catalog, probe) {
+    return catalog.map((check) => {
+        const result = probe(check.packageName);
+        if (result.ok) {
+            return { ...check, status: 'loaded' };
+        }
+        const missingModule = isModuleNotFound(result.error);
+        const status = check.required
+            ? 'required-missing'
+            : missingModule
+                ? 'missing'
+                : 'missing';
+        return { ...check, status, loadError: result.error.message };
+    });
+}
+function isModuleNotFound(err) {
+    return err.code === 'MODULE_NOT_FOUND';
+}
+// ============================================================================
+// Environment overrides
+// ============================================================================
+/**
+ * Map of RUVECTOR_* env vars → feature flag names that aqe upgrade cares about.
+ * Only includes flags tied to optional natives — the full list is in
+ * feature-flags.ts.
+ */
+const ENV_VAR_TO_FLAG = {
+    RUVECTOR_USE_RVF_PATTERN_STORE: 'useRVFPatternStore',
+    RUVECTOR_USE_SUBLINEAR_SOLVER: 'useSublinearSolver',
+    RUVECTOR_USE_NATIVE_HNSW: 'useNativeHNSW',
+    RUVECTOR_USE_GNN_INDEX: 'useQEGNNIndex',
+    RUVECTOR_USE_FLASH_ATTENTION: 'useQEFlashAttention',
+    RUVECTOR_USE_GRAPH_MAE_EMBEDDINGS: 'useGraphMAEEmbeddings',
+};
+export function readEnvOverrides(env) {
+    const out = [];
+    for (const [envVar, flagName] of Object.entries(ENV_VAR_TO_FLAG)) {
+        const v = env[envVar];
+        if (v !== undefined)
+            out.push({ envVar, value: v, flagName });
+    }
+    return out;
+}
+export function buildRecommendations(input) {
+    const recs = [];
+    const nativeByName = new Map(input.natives.map((n) => [n.packageName, n]));
+    // Missing required deps are a hard error.
+    for (const n of input.natives) {
+        if (n.status === 'required-missing') {
+            recs.push({
+                severity: 'error',
+                message: `Required dependency missing: ${n.packageName} — ${n.role}`,
+                action: `npm install ${n.packageName}`,
+            });
+        }
+    }
+    // Missing optional deps: suggest install, note fallback.
+    for (const n of input.natives) {
+        if (n.status === 'missing' && !n.required) {
+            recs.push({
+                severity: 'warn',
+                message: `Optional native missing: ${n.packageName} — falls back to ${n.fallback}`,
+                action: `npm install ${n.packageName}`,
+            });
+        }
+    }
+    // Env override conflicts: user forced a flag ON but the native isn't loadable.
+    const flagByName = { ...input.flags };
+    for (const override of input.envOverrides) {
+        const natives = input.natives.filter((n) => n.affectsFlags.includes(override.flagName));
+        const anyLoaded = natives.some((n) => n.status === 'loaded');
+        const wantsOn = override.value === 'true' || override.value === '1';
+        if (wantsOn && natives.length > 0 && !anyLoaded) {
+            const missing = natives.map((n) => n.packageName).join(', ');
+            recs.push({
+                severity: 'warn',
+                message: `${override.envVar}=${override.value} requests flag ${override.flagName}=true, ` +
+                    `but required native(s) not loaded: ${missing}. The flag will silently fall back.`,
+                action: natives[0] ? `npm install ${natives[0].packageName}` : undefined,
+            });
+        }
+    }
+    void flagByName; // reserved for future rules
+    void nativeByName;
+    // All optionals loaded → positive-confirmation info line.
+    const optionalMissing = input.natives.filter((n) => !n.required && n.status === 'missing');
+    if (optionalMissing.length === 0 && input.natives.every((n) => n.status !== 'required-missing')) {
+        recs.push({
+            severity: 'info',
+            message: 'All recommended native bindings are loaded — no action required.',
+        });
+    }
+    return recs;
+}
+export function buildReport(input) {
+    const natives = detectNatives(NATIVE_CATALOG, input.probe);
+    const envOverrides = readEnvOverrides(input.env);
+    const recommendations = buildRecommendations({
+        natives,
+        flags: input.flags,
+        envOverrides,
+    });
+    const optionalLoadedCount = natives.filter((n) => !n.required && n.status === 'loaded').length;
+    const optionalMissingCount = natives.filter((n) => !n.required && n.status === 'missing').length;
+    const requiredOk = natives.filter((n) => n.required).every((n) => n.status === 'loaded');
+    return {
+        aqeVersion: input.aqeVersion,
+        platform: {
+            os: platform(),
+            arch: arch(),
+            node: process.version,
+        },
+        natives,
+        flags: input.flags,
+        envOverrides,
+        recommendations,
+        summary: {
+            requiredOk,
+            optionalMissingCount,
+            optionalLoadedCount,
+        },
+    };
+}
+// ============================================================================
+// Exit-code policy
+// ============================================================================
+export function exitCodeFor(report, strict) {
+    if (!report.summary.requiredOk)
+        return 2;
+    if (strict && report.summary.optionalMissingCount > 0)
+        return 1;
+    return 0;
+}
+// ============================================================================
+// Rendering
+// ============================================================================
+export function renderReportHuman(report) {
+    const lines = [];
+    const push = (s = '') => lines.push(s);
+    push('');
+    push(chalk.bold.blue('  aqe upgrade — native binding report'));
+    push(chalk.gray('  ──────────────────────────────────────'));
+    push('');
+    push(`  AQE:       ${chalk.cyan(report.aqeVersion)}`);
+    push(`  Platform:  ${chalk.cyan(`${report.platform.os} ${report.platform.arch}`)}`);
+    push(`  Node:      ${chalk.cyan(report.platform.node)}`);
+    push('');
+    push(chalk.blue('  Native bindings:'));
+    for (const n of report.natives) {
+        const status = statusBadge(n.status);
+        push(`    ${status} ${chalk.bold(n.packageName.padEnd(28))} ${chalk.gray(n.role)}`);
+        if (n.status !== 'loaded' && n.loadError) {
+            // Node's MODULE_NOT_FOUND error message carries a multi-line "Require
+            // stack:" trailer that adds no signal here — keep the first line only.
+            push(`        ${chalk.gray(n.loadError.split('\n')[0])}`);
+        }
+    }
+    push('');
+    push(chalk.blue('  Flag state (after env overrides):'));
+    const flagEntries = Object.entries(report.flags);
+    for (const [name, value] of flagEntries) {
+        const badge = value ? chalk.green('on ') : chalk.yellow('off');
+        push(`    ${badge}  ${name}`);
+    }
+    if (report.envOverrides.length > 0) {
+        push('');
+        push(chalk.blue('  Env overrides in effect:'));
+        for (const o of report.envOverrides) {
+            push(`    ${chalk.cyan(o.envVar)}=${chalk.cyan(o.value)}  ${chalk.gray(`→ ${o.flagName}`)}`);
+        }
+    }
+    push('');
+    push(chalk.blue('  Recommendations:'));
+    if (report.recommendations.length === 0) {
+        push(chalk.gray('    (none)'));
+    }
+    else {
+        for (const rec of report.recommendations) {
+            const prefix = recommendationPrefix(rec.severity);
+            push(`    ${prefix} ${rec.message}`);
+            if (rec.action)
+                push(`        ${chalk.gray('→')} ${chalk.cyan(rec.action)}`);
+        }
+    }
+    push('');
+    const okBadge = report.summary.requiredOk ? chalk.green('OK') : chalk.red('FAIL');
+    push(`  Summary:   required ${okBadge}    ` +
+        `optional loaded ${chalk.cyan(report.summary.optionalLoadedCount)} / ` +
+        `${chalk.cyan(report.summary.optionalLoadedCount + report.summary.optionalMissingCount)}`);
+    push('');
+    return lines.join('\n');
+}
+function statusBadge(status) {
+    switch (status) {
+        case 'loaded':
+            return chalk.green('✓');
+        case 'missing':
+            return chalk.yellow('…');
+        case 'required-missing':
+            return chalk.red('✗');
+    }
+}
+function recommendationPrefix(severity) {
+    switch (severity) {
+        case 'info':
+            return chalk.green('✓');
+        case 'warn':
+            return chalk.yellow('!');
+        case 'error':
+            return chalk.red('✗');
+    }
+}
+export function createUpgradeCommand(cleanupAndExit) {
+    const cmd = new Command('upgrade')
+        .description('Detect optional native bindings and recommend install / flag changes (read-only)')
+        .option('--json', 'Emit the report as JSON to stdout', false)
+        .option('--strict', 'Exit non-zero if any recommended optional native is missing', false)
+        .action(async (options) => {
+        const aqeVersion = resolveAqeVersion();
+        const rvFlags = getRuVectorFeatureFlags();
+        const report = buildReport({
+            aqeVersion,
+            probe: createDefaultLoadProbe(),
+            env: process.env,
+            flags: {
+                useRVFPatternStore: rvFlags.useRVFPatternStore,
+                useSublinearSolver: rvFlags.useSublinearSolver,
+                useNativeHNSW: rvFlags.useNativeHNSW,
+                useGraphMAEEmbeddings: rvFlags.useGraphMAEEmbeddings,
+                useQEFlashAttention: rvFlags.useQEFlashAttention,
+            },
+        });
+        if (options.json) {
+            process.stdout.write(JSON.stringify(report, null, 2) + '\n');
+        }
+        else {
+            process.stdout.write(renderReportHuman(report));
+        }
+        await cleanupAndExit(exitCodeFor(report, options.strict === true));
+    });
+    return cmd;
+}
+// ============================================================================
+// Helpers
+// ============================================================================
+function resolveAqeVersion() {
+    try {
+        const req = createRequire(import.meta.url);
+        const pkg = req('../../../package.json');
+        return pkg.version ?? 'unknown';
+    }
+    catch {
+        return 'unknown';
+    }
+}
+//# sourceMappingURL=upgrade.js.map

package/dist/cli/completions/index.d.ts

@@ -152,6 +152,33 @@ export declare const COMMANDS: {
             };
         };
     };
+    readonly brain: {
+        readonly description: "Export, import, and inspect QE brain state";
+        readonly subcommands: {
+            readonly export: {
+                readonly options: readonly ["-o", "--output", "--format", "--db"];
+            };
+            readonly import: {
+                readonly options: readonly ["-i", "--input", "--strategy", "--dry-run", "--db"];
+            };
+            readonly info: {
+                readonly options: readonly ["-i", "--input"];
+            };
+            readonly diff: {
+                readonly options: readonly ["--table", "--verbose", "--json"];
+            };
+            readonly search: {
+                readonly options: readonly ["-i", "--input", "--table", "--domain", "--pattern-type", "--since", "--until", "-q", "--query", "-l", "--limit", "--json"];
+            };
+            readonly 'witness-backfill': {
+                readonly options: readonly ["--db"];
+            };
+        };
+    };
+    readonly upgrade: {
+        readonly description: "Detect optional native bindings and recommend install / flag changes";
+        readonly options: readonly ["--json", "--strict"];
+    };
 };
 /**
  * Task types for completion