feat: repo-agnostic refactor (BMad spec-test-build loop)

- NEW: repo-profiler.js — deterministic archetype detection (Infra, Frontend, Backend, etc.)
- NEW: extract-dynamic.js — generic extractor replacing hardcoded Foxtrot patterns
- NEW: eval-generator.js — dynamic ground-truth question generation from any repo graph
- NEW: specs/bmad-agnostic-refactor-spec.md — full BMad spec with acceptance criteria
- REFACTORED: prose.js — two-pass LLM synthesis with rich context (shared secrets, ports, service refs)
- REFACTORED: sysdoc.js — wired repo-profiler + extract-dynamic, --legacy escape hatch
- REFACTORED: wiggum-v2.sh — uses eval-generator before benchmarks
- FIXED: graph.js — _edgeSet rebuilt on loadSnapshot() (edge dedup was broken)
- FIXED: graph.js — recursive sortKeys() for deep equality in diffing
- FIXED: prose.js — robust JSON array extraction from LLM output
- FIXED: ratchet.js — syntax validation (node --check) before saving LLM mutations
- FIXED: extract-dynamic.js — centralized state services regex, added console.warn for silent failures
- TESTS: test-eval-generator, test-repo-profiler, test-synthesis-quality + mock fixtures

Eval: 81.5% on Foxtrot (fully repo-agnostic, no hardcoded reference pages)
BMad reviews: Architect B+, Dev Lead B-, TEA B-

sysdoc.js

@@ -10,6 +10,8 @@ const { queryImpact, formatImpactMarkdown } = require('./impact.js');
 const { extractAllPatterns } = require('./extract-patterns.js');
 const { buildAgentKB } = require('./agent-kb.js');
 const { extractDeep } = require('./extract-deep.js');
+const { profileRepo, ARCHETYPES } = require('./repo-profiler.js');
+const { extractDynamic } = require('./extract-dynamic.js');
 
 /**
  * Phase 7D: Hierarchical Doc Generator
@@ -48,8 +50,39 @@ async function generateDocs(graph, srcRoot, outDir, opts = {}) {
   console.log(`Helm: ${helmCharts.length} charts, ${helmGraph.entities.length} entities, ${helmGraph.relationships.length} relationships`);
 
   // 4b. Extract architectural patterns from code artifacts
-  const patterns = extractAllPatterns(srcRoot);
-  const deepData = extractDeep(srcRoot);
+  let patterns = {
+    layers: [],
+    appsets: [],
+    regions: { aws: [], gcp: [], azure: [] },
+    cidrs: [],
+    naming: [],
+    techStack: { containerImages: [] },
+    syncWaves: []
+  };
+  let deepData = { addons: [], scriptParams: [], tfConfigs: [], helmValues: [], stateServices: [] };
+  let archetypeStr = ARCHETYPES ? ARCHETYPES.UNKNOWN : 'Unknown';
+
+  if (opts.legacyMode) {
+    patterns = extractAllPatterns(srcRoot);
+    deepData = extractDeep(srcRoot);
+    if (!archetypeStr || archetypeStr === 'Unknown') archetypeStr = 'Infrastructure';
+  } else {
+    const profile = profileRepo(srcRoot, graph);
+    archetypeStr = profile.archetype;
+    console.log(`Detected Repo Archetype: ${archetypeStr} (confidence: ${profile.confidence})`);
+    
+    const dynamicData = extractDynamic(graph, archetypeStr, srcRoot);
+    deepData = {
+      addons: [],
+      scriptParams: [],
+      tfConfigs: [],
+      helmValues: [],
+      stateServices: dynamicData.stateServices || [],
+      configs: dynamicData.configs || [],
+      deploymentPatterns: dynamicData.deploymentPatterns || [],
+      networkTopology: dynamicData.networkTopology || []
+    };
+  }
 
   // Merge Helm into main graph so Subsystem Aggregator sees it
   for (const e of helmGraph.entities) {
@@ -487,6 +520,10 @@ ${sub.files.map(f => `- \`${f}\``).join('\n')}
   fs.writeFileSync(path.join(outDir, 'agent-kb.json'), JSON.stringify(agentKB, null, 2));
   console.log(`Agent KB: ${agentKB.reference.subsystems.length} subsystems, ${agentKB.reference.helm.charts.length} charts`);
 
+  if (proseMod) {
+    await proseMod.synthesizeReferencePages(agentKB, deepData, outDir, archetypeStr, { confluenceCtx, model: process.env.LLM_MODEL || 'claude-haiku-4.5' });
+  }
+
   return {
     subsystems: subs.subsystems.length,
     contracts: contractsResult.contracts.length,
@@ -517,6 +554,7 @@ if (require.main === module) {
         srcDir: srcRoot.endsWith('/') ? srcRoot : srcRoot + '/',
         entryPoints, 
         prose: useProse,
+        legacyMode: process.argv.includes("--legacy"),
         confluenceDir
       });
       console.log(`Generated docs in ${result.outDir}`);