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/cli/commands/cow.ts

@@ -274,74 +274,7 @@ ${chalk.cyan('Fork Statistics:')}
   },
 
   /**
-   * Merge a fork/branch into current branch
-   */
-  async merge(source: string | undefined, target: string | undefined, options: MergeOptions) {
-    let spinner: any = null
-    try {
-      const brain = getBrainy()
-      await brain.init()
-
-      // Interactive mode if parameters missing
-      if (!source || !target) {
-        const branches = await brain.listBranches()
-        const currentBranch = await brain.getCurrentBranch()
-
-        const answers = await inquirer.prompt([
-          {
-            type: 'list',
-            name: 'source',
-            message: 'Merge FROM branch:',
-            choices: branches.map(b => ({ name: b, value: b })),
-            when: !source
-          },
-          {
-            type: 'list',
-            name: 'target',
-            message: 'Merge INTO branch:',
-            choices: branches.map(b => ({
-              name: b === currentBranch ? `${b} (current)` : b,
-              value: b
-            })),
-            default: currentBranch,
-            when: !target
-          }
-        ])
-
-        source = source || answers.source
-        target = target || answers.target
-      }
-
-      spinner = ora(`Merging ${chalk.cyan(source)} → ${chalk.green(target)}...`).start()
-
-      const result = await brain.merge(source!, target!, {
-        strategy: options.strategy || 'last-write-wins'
-      })
-
-      spinner.succeed(`Merged ${chalk.cyan(source)} → ${chalk.green(target)}`)
-
-      console.log(`
-${chalk.cyan('Merge Summary:')}
-  ${chalk.green('Added:')} ${result.added} entities
-  ${chalk.yellow('Modified:')} ${result.modified} entities
-  ${chalk.red('Deleted:')} ${result.deleted} entities
-  ${chalk.magenta('Conflicts:')} ${result.conflicts} (resolved)
-      `.trim())
-
-      if (options.json) {
-        formatOutput(result, options)
-      }
-
-    } catch (error: any) {
-      if (spinner) spinner.fail('Merge failed')
-      console.error(chalk.red('Error:'), error.message)
-      if (options.verbose) console.error(error)
-      process.exit(1)
-    }
-  },
-
-  /**
-   * Get commit history
+   * View commit history
    */
   async history(options: CoreOptions & { limit?: string }) {
     try {

src/cli/commands/data.ts

@@ -1,7 +1,7 @@
 /**
  * Data Management Commands
  *
- * Backup, restore, import, export operations
+ * Import, export, and statistics operations
  */
 
 import chalk from 'chalk'
@@ -31,87 +31,6 @@ const formatOutput = (data: any, options: DataOptions): void => {
 }
 
 export const dataCommands = {
-  /**
-   * Backup database
-   */
-  async backup(file: string, options: DataOptions & { compress?: boolean }) {
-    const spinner = ora('Creating backup...').start()
-
-    try {
-      const brain = getBrainy()
-      const dataApi = await brain.data()
-
-      const backup = await dataApi.backup({
-        compress: options.compress
-      })
-
-      spinner.text = 'Writing backup file...'
-
-      // Write backup to file
-      const content = typeof backup === 'string'
-        ? backup
-        : JSON.stringify(backup, null, options.pretty ? 2 : 0)
-
-      writeFileSync(file, content)
-
-      spinner.succeed('Backup created')
-
-      if (!options.json) {
-        console.log(chalk.green(`✓ Backup saved to: ${file}`))
-        if ((backup as any).compressed) {
-          console.log(chalk.dim(`  Original size: ${formatBytes((backup as any).originalSize)}`))
-          console.log(chalk.dim(`  Compressed size: ${formatBytes((backup as any).compressedSize)}`))
-          console.log(chalk.dim(`  Compression ratio: ${(((backup as any).compressedSize / (backup as any).originalSize) * 100).toFixed(1)}%`))
-        }
-      } else {
-        formatOutput({ file, backup: true }, options)
-      }
-    } catch (error: any) {
-      spinner.fail('Backup failed')
-      console.error(chalk.red(error.message))
-      process.exit(1)
-    }
-  },
-
-  /**
-   * Restore from backup
-   */
-  async restore(file: string, options: DataOptions & { merge?: boolean }) {
-    const spinner = ora('Restoring from backup...').start()
-
-    try {
-      const brain = getBrainy()
-      const dataApi = await brain.data()
-
-      // Read backup file
-      const content = readFileSync(file, 'utf-8')
-      const backup = JSON.parse(content)
-
-      // Restore
-      await dataApi.restore({
-        backup,
-        merge: options.merge || false
-      })
-
-      spinner.succeed('Restore complete')
-
-      if (!options.json) {
-        console.log(chalk.green(`✓ Restored from: ${file}`))
-        if (options.merge) {
-          console.log(chalk.dim('  Mode: Merged with existing data'))
-        } else {
-          console.log(chalk.dim('  Mode: Replaced all data'))
-        }
-      } else {
-        formatOutput({ file, restored: true }, options)
-      }
-    } catch (error: any) {
-      spinner.fail('Restore failed')
-      console.error(chalk.red(error.message))
-      process.exit(1)
-    }
-  },
-
   /**
    * Get database statistics
    */

src/cli/index.ts

@@ -536,18 +536,8 @@ program
 
 // ===== Data Management Commands =====
 
-program
-  .command('backup <file>')
-  .description('Create database backup')
-  .option('--compress', 'Compress backup')
-  .action(dataCommands.backup)
 
 program
-  .command('restore <file>')
-  .description('Restore from backup')
-  .option('--merge', 'Merge with existing data (default: replace)')
-  .action(dataCommands.restore)
-
 program
   .command('data-stats')
   .description('Show detailed database statistics')
@@ -657,13 +647,6 @@ program
   .description('Switch to a different branch')
   .action(cowCommands.checkout)
 
-program
-  .command('merge [source] [target]')
-  .description('Merge a fork/branch into another branch')
-  .option('--strategy <type>', 'Merge strategy (last-write-wins|custom)', 'last-write-wins')
-  .option('-f, --force', 'Force merge on conflicts')
-  .action(cowCommands.merge)
-
 program
   .command('history')
   .alias('log')