chore: recovery checkpoint - v3.0 API successfully recovered

CRITICAL CHECKPOINT - DO NOT PUSH TO GITHUB

Recovery Status:
- Successfully recovered brainy.ts from compiled JavaScript
- All core v3.0 API methods functional (add, get, update, delete, relate, find, etc.)
- Neural subsystem intact (562KB embedded patterns, NLP working)
- Augmentation pipeline operational (20+ augmentations)
- HNSW clustering system complete
- Triple Intelligence compiled (needs constructor fix)
- Test suite validates functionality

Changes preserved:
- 898 files with changes from last 3 days
- 144,475 insertions
- All augmentation improvements
- All test coverage enhancements
- Complete v3.0 feature set

This is a LOCAL checkpoint only - contains recovered work after corruption incident.
Created backup in .backups/brainy-full-20250910-151314.tar.gz

Branch: recovery-checkpoint-20250910-151433
Date: Wed Sep 10 03:18:04 PM PDT 2025

.recovery-workspace/dist-backup-20250910-141917/utils/deletedItemsIndex.d.ts

@@ -0,0 +1,59 @@
+/**
+ * Dedicated index for tracking soft-deleted items
+ * This is MUCH more efficient than checking every item in the database
+ *
+ * Performance characteristics:
+ * - Add deleted item: O(1)
+ * - Remove deleted item: O(1)
+ * - Check if deleted: O(1)
+ * - Get all deleted: O(d) where d = number of deleted items << total items
+ */
+export declare class DeletedItemsIndex {
+    private deletedIds;
+    private deletedCount;
+    /**
+     * Mark an item as deleted
+     */
+    markDeleted(id: string): void;
+    /**
+     * Mark an item as not deleted (restored)
+     */
+    markRestored(id: string): void;
+    /**
+     * Check if an item is deleted - O(1)
+     */
+    isDeleted(id: string): boolean;
+    /**
+     * Get all deleted item IDs - O(d)
+     */
+    getAllDeleted(): string[];
+    /**
+     * Filter out deleted items from results - O(k) where k = result count
+     */
+    filterDeleted<T extends {
+        id?: string;
+    }>(items: T[]): T[];
+    /**
+     * Get statistics
+     */
+    getStats(): {
+        deletedCount: number;
+        memoryUsage: number;
+    };
+    /**
+     * Clear all deleted items (for testing)
+     */
+    clear(): void;
+    /**
+     * Serialize for persistence
+     */
+    serialize(): string;
+    /**
+     * Deserialize from persistence
+     */
+    deserialize(data: string): void;
+}
+/**
+ * Global singleton for deleted items tracking
+ */
+export declare const deletedItemsIndex: DeletedItemsIndex;