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/ensureDeleted.js

@@ -0,0 +1,79 @@
+/**
+ * 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, preserveExisting = true) {
+    // 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) {
+    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) {
+    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) {
+    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) {
+    // 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`;
+//# sourceMappingURL=ensureDeleted.js.map