feat: ID-first storage architecture + remove memory-unsafe APIs (v6.0.0)

BREAKING CHANGES:

**ID-First Storage Paths**
- Direct O(1) entity access without type lookups
- Before: entities/nouns/{TYPE}/metadata/{SHARD}/{ID}.json
- After:  entities/nouns/{SHARD}/{ID}/metadata.json
- Migration handled automatically on first init()

**Removed Memory-Unsafe APIs**
- Removed brain.merge() - loaded all entities into memory
- Removed brain.diff() - loaded all entities into memory
- Removed brain.data().backup() - loaded all entities into memory
- Removed brain.data().restore() - depended on backup()
- Removed CLI commands: backup, restore, cow merge

**Migration Paths**
- merge() → Use checkout() or manually copy entities with pagination
- diff() → Use asOf() with manual paginated comparison
- backup() → Use fork() for instant COW snapshots
- restore() → Use checkout() to switch to snapshot branch

Core Improvements:
- ✅ All 8 storage adapters properly call super.init()
- ✅ GraphAdjacencyIndex integration in BaseStorage.init()
- ✅ Fixed ID-first path bugs (vector.json → vectors.json)
- ✅ Fixed MemoryStorage.initializeCounts() for ID-first paths
- ✅ New VFS APIs: du(), access(), find()
- ✅ Comprehensive documentation with migration guides

Storage Adapters Fixed:
- MemoryStorage, FileSystemStorage, AzureBlobStorage
- GCSStorage, R2Storage, S3CompatibleStorage
- OPFSStorage, HistoricalStorageAdapter

Files Changed: 28 files, +1,075/-1,933 lines (net -858)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/neural/embeddedTypeEmbeddings.ts

@@ -2,7 +2,7 @@
  * 🧠 BRAINY EMBEDDED TYPE EMBEDDINGS
  *
  * AUTO-GENERATED - DO NOT EDIT
- * Generated: 2025-11-06T17:38:22.619Z
+ * Generated: 2025-11-19T21:22:15.103Z
  * Noun Types: 42
  * Verb Types: 127
  *
@@ -19,7 +19,7 @@ export const TYPE_METADATA = {
   verbTypes: 127,
   totalTypes: 169,
   embeddingDimensions: 384,
-  generatedAt: "2025-11-06T17:38:22.619Z",
+  generatedAt: "2025-11-19T21:22:15.103Z",
   sizeBytes: {
     embeddings: 259584,
     base64: 346112