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.js

@@ -0,0 +1,98 @@
+/**
+ * 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 class DeletedItemsIndex {
+    constructor() {
+        this.deletedIds = new Set();
+        this.deletedCount = 0;
+    }
+    /**
+     * Mark an item as deleted
+     */
+    markDeleted(id) {
+        if (!this.deletedIds.has(id)) {
+            this.deletedIds.add(id);
+            this.deletedCount++;
+        }
+    }
+    /**
+     * Mark an item as not deleted (restored)
+     */
+    markRestored(id) {
+        if (this.deletedIds.delete(id)) {
+            this.deletedCount--;
+        }
+    }
+    /**
+     * Check if an item is deleted - O(1)
+     */
+    isDeleted(id) {
+        return this.deletedIds.has(id);
+    }
+    /**
+     * Get all deleted item IDs - O(d)
+     */
+    getAllDeleted() {
+        return Array.from(this.deletedIds);
+    }
+    /**
+     * Filter out deleted items from results - O(k) where k = result count
+     */
+    filterDeleted(items) {
+        if (this.deletedCount === 0) {
+            // Fast path - no deleted items
+            return items;
+        }
+        return items.filter(item => {
+            const id = item.id;
+            return id ? !this.deletedIds.has(id) : true;
+        });
+    }
+    /**
+     * Get statistics
+     */
+    getStats() {
+        return {
+            deletedCount: this.deletedCount,
+            memoryUsage: this.deletedCount * 100 // Rough estimate: 100 bytes per ID
+        };
+    }
+    /**
+     * Clear all deleted items (for testing)
+     */
+    clear() {
+        this.deletedIds.clear();
+        this.deletedCount = 0;
+    }
+    /**
+     * Serialize for persistence
+     */
+    serialize() {
+        return JSON.stringify(Array.from(this.deletedIds));
+    }
+    /**
+     * Deserialize from persistence
+     */
+    deserialize(data) {
+        try {
+            const ids = JSON.parse(data);
+            this.deletedIds = new Set(ids);
+            this.deletedCount = this.deletedIds.size;
+        }
+        catch (e) {
+            console.warn('Failed to deserialize deleted items index');
+        }
+    }
+}
+/**
+ * Global singleton for deleted items tracking
+ */
+export const deletedItemsIndex = new DeletedItemsIndex();
+//# sourceMappingURL=deletedItemsIndex.js.map