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>

README.md

@@ -296,12 +296,8 @@ await experiment.updateAll({ /* migration logic */ })
 // Commit your work
 await experiment.commit({ message: 'Add test user', author: 'dev@example.com' })
 
-// Merge back to main with conflict resolution
-const result = await brain.merge('test-migration', 'main', {
-  strategy: 'last-write-wins'
-})
-
-console.log(result)  // { added: 1, modified: 0, conflicts: 0 }
+// Switch to experimental branch to make it active
+await brain.checkout('test-migration')
 
 // Time-travel: Query database at any past commit (read-only)
 const commits = await brain.getHistory({ limit: 10 })