Add deep extractors, reference pages, keyword index; eval 53.3%

- extract-deep.js: mines addon versions, TF configs, script params, helm values, state services
- generate-reference-pages.js: creates operations.md, configuration.md, network-architecture.md
- reference/index.md: keyword-rich topic-to-file routing table
- Enriched CIDR extractor with inline comment capture
- Eval progression: 28.7% -> 33.4% -> 46.7% -> 52.5% -> 53.3%
- NOT_FOUND: 25 -> 20 -> 16 -> 10 -> 11
- Top scores: config-region-code 95%, argo-gen-params 95%, multiple 100%s
- Remaining gap: agent planner (haiku) doesn't consistently follow index routing

sysdoc.js

@@ -9,6 +9,7 @@ const { discoverCharts, chartsToGraph, generateHelmDiagram } = require('./extrac
 const { queryImpact, formatImpactMarkdown } = require('./impact.js');
 const { extractAllPatterns } = require('./extract-patterns.js');
 const { buildAgentKB } = require('./agent-kb.js');
+const { extractDeep } = require('./extract-deep.js');
 
 /**
  * Phase 7D: Hierarchical Doc Generator
@@ -48,6 +49,7 @@ async function generateDocs(graph, srcRoot, outDir, opts = {}) {
 
   // 4b. Extract architectural patterns from code artifacts
   const patterns = extractAllPatterns(srcRoot);
+  const deepData = extractDeep(srcRoot);
 
   // Merge Helm into main graph so Subsystem Aggregator sees it
   for (const e of helmGraph.entities) {
@@ -182,6 +184,17 @@ ${patterns.naming.slice(0, 15).map(n => `- \`${n.pattern}\` (via \`${n.file}\`)`
 **Core Images:**
 ${patterns.techStack.containerImages.slice(0, 20).map(i => `- \`${i}\``).join('\n')}
 
+## Configuration & Operational Defaults
+**State Management Services:** ${deepData.stateServices.map(s => s.name).filter((v, i, a) => a.indexOf(v) === i).join(', ')}
+**Cluster Addons (EKS/GKE):**
+${deepData.addons.map(a => `- ${a.name}: ${a.version}`).join('\n')}
+**Key Script Parameters (Timeouts/Retries):**
+${deepData.scriptParams.filter(p => p.name.includes('TIMEOUT') || p.name.includes('WAIT')).map(p => `- ${p.name} = ${p.value} (${p.file})`).join('\n')}
+**Infrastructure Configs:**
+${deepData.tfConfigs.filter(c => c.key.includes('backup')).map(c => `- ${c.key}: ${c.value} (${c.file})`).join('\n')}
+**Account/Template Values:**
+${deepData.helmValues.map(v => `- ${v.key}: ${v.value} (${v.file})`).join('\n')}
+
 ## Subsystems
 
 | Subsystem | Kind | Files | Modules | Functions |
@@ -472,7 +485,7 @@ ${sub.files.map(f => `- \`${f}\``).join('\n')}
   // Generate Agent Knowledge Base (JSON)
   const agentKB = buildAgentKB(graph, srcRoot, helmCharts, subs, contractsResult, patterns, impactResults);
   fs.writeFileSync(path.join(outDir, 'agent-kb.json'), JSON.stringify(agentKB, null, 2));
-  console.log(`Agent KB: ${agentKB.facts.length} facts indexed`);
+  console.log(`Agent KB: ${agentKB.reference.subsystems.length} subsystems, ${agentKB.reference.helm.charts.length} charts`);
 
   return {
     subsystems: subs.subsystems.length,