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-

graph.js

@@ -82,15 +82,29 @@ class GraphStore {
      * @returns {GraphStore}
      */
     static loadSnapshot(inputPath) {
-        const data = JSON.parse(fs.readFileSync(inputPath, 'utf8'));
+        let data;
+        if (typeof inputPath === 'string') {
+            data = JSON.parse(fs.readFileSync(inputPath, 'utf8'));
+        } else {
+            data = inputPath; // Allow passing the parsed object directly
+        }
         const graph = new GraphStore();
         
         for (const [id, entity] of Object.entries(data.nodes || {})) {
             graph.nodes.set(id, entity);
+            const filePath = entity._file || entity.path;
+            if (!data.fileIndex && filePath) {
+                if (!graph.fileIndex.has(filePath)) graph.fileIndex.set(filePath, new Set());
+                graph.fileIndex.get(filePath).add(id);
+            }
         }
         
         graph.edges = data.edges || [];
         
+        for (const e of graph.edges) {
+            graph._edgeSet.add(`${e.type}:${e.source}->${e.target}`);
+        }
+        
         for (const [filePath, entityIds] of Object.entries(data.fileIndex || {})) {
             graph.fileIndex.set(filePath, new Set(entityIds));
         }
@@ -184,7 +198,17 @@ class GraphStore {
                 diff.entities.added.push(newEntity);
             } else {
                 // Deterministic deep comparison: sort keys, compare canonical JSON
-                const canonicalize = (obj) => JSON.stringify(obj, Object.keys(obj).filter(k => k !== '_file').sort());
+                const sortKeys = (obj) => {
+                  if (Array.isArray(obj)) return obj.map(sortKeys);
+                  if (obj && typeof obj === 'object') {
+                    return Object.keys(obj).filter(k => k !== '_file').sort().reduce((acc, key) => {
+                      acc[key] = sortKeys(obj[key]);
+                      return acc;
+                    }, {});
+                  }
+                  return obj;
+                };
+                const canonicalize = (obj) => JSON.stringify(sortKeys(obj));
                 if (canonicalize(oldEntity) !== canonicalize(newEntity)) {
                     diff.entities.modified.push({ old: oldEntity, new: newEntity });
                 }