feat: comprehensive metadata namespace architecture and cleanup system

BREAKING CHANGE: Remove hard delete option from deleteVerb() for consistent API

- Add complete metadata namespace architecture with O(1) soft delete performance
- Implement periodic cleanup system for old soft-deleted items
- Add restore methods for both nouns and verbs
- Require metadata contracts for all augmentations
- Eliminate namespace collisions with clean separation (_brainy, _augmentations, _audit)
- Optimize index performance using flattened dot-notation for O(1) lookups
- Add comprehensive augmentation safety system with type-safe access control
- Maintain full backward compatibility for existing data
- Add enterprise-grade cleanup with configurable age thresholds and batch processing

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

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

src/utils/ensureDeleted.ts

@@ -0,0 +1,88 @@
+/**
+ * Utility to ensure all metadata has the deleted field set properly
+ * This is CRITICAL for O(1) soft delete filtering performance
+ * 
+ * Uses _brainy namespace to avoid conflicts with user metadata
+ */
+
+const BRAINY_NAMESPACE = '_brainy'
+
+/**
+ * Ensure metadata has internal Brainy fields set
+ * @param metadata The metadata object (could be null/undefined)
+ * @param preserveExisting If true, preserve existing deleted value
+ * @returns Metadata with internal fields guaranteed
+ */
+export function ensureDeletedField(metadata: any, preserveExisting: boolean = true): any {
+  // Handle null/undefined metadata
+  if (!metadata) {
+    return { 
+      [BRAINY_NAMESPACE]: {
+        deleted: false,
+        version: 1
+      }
+    }
+  }
+  
+  // Clone to avoid mutation
+  const result = { ...metadata }
+  
+  // Ensure _brainy namespace exists
+  if (!result[BRAINY_NAMESPACE]) {
+    result[BRAINY_NAMESPACE] = {}
+  }
+  
+  // Set deleted field if not present
+  if (!('deleted' in result[BRAINY_NAMESPACE])) {
+    result[BRAINY_NAMESPACE].deleted = false
+  } else if (!preserveExisting) {
+    // Force to false if not preserving
+    result[BRAINY_NAMESPACE].deleted = false
+  }
+  
+  return result
+}
+
+/**
+ * Mark an item as soft deleted
+ * @param metadata The metadata object
+ * @returns Metadata with _brainy.deleted=true
+ */
+export function markAsDeleted(metadata: any): any {
+  const result = ensureDeletedField(metadata)
+  result[BRAINY_NAMESPACE].deleted = true
+  return result
+}
+
+/**
+ * Mark an item as restored (not deleted)
+ * @param metadata The metadata object  
+ * @returns Metadata with _brainy.deleted=false
+ */
+export function markAsRestored(metadata: any): any {
+  const result = ensureDeletedField(metadata)
+  result[BRAINY_NAMESPACE].deleted = false
+  return result
+}
+
+/**
+ * Check if an item is deleted
+ * @param metadata The metadata object
+ * @returns true if deleted, false otherwise (including if field missing)
+ */
+export function isDeleted(metadata: any): boolean {
+  return metadata?.[BRAINY_NAMESPACE]?.deleted === true
+}
+
+/**
+ * Check if an item is active (not deleted)
+ * @param metadata The metadata object
+ * @returns true if not deleted (default), false if deleted
+ */
+export function isActive(metadata: any): boolean {
+  // If no deleted field or deleted=false, item is active
+  return !isDeleted(metadata)
+}
+
+// Export the namespace constant for use in queries
+export const BRAINY_DELETED_FIELD = `${BRAINY_NAMESPACE}.deleted`