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/metadataNamespace.js

@@ -0,0 +1,162 @@
+/**
+ * Clean Metadata Architecture for Brainy 2.2
+ * No backward compatibility - doing it RIGHT from the start!
+ */
+// Namespace constants
+export const BRAINY_NS = '_brainy';
+export const AUG_NS = '_augmentations';
+export const AUDIT_NS = '_audit';
+// Field paths for O(1) indexing
+export const DELETED_FIELD = `${BRAINY_NS}.deleted`;
+export const INDEXED_FIELD = `${BRAINY_NS}.indexed`;
+export const VERSION_FIELD = `${BRAINY_NS}.version`;
+/**
+ * Create properly namespaced metadata
+ * This is called for EVERY noun/verb creation
+ */
+export function createNamespacedMetadata(userMetadata) {
+    const now = Date.now();
+    // Start with user metadata or empty object
+    const result = userMetadata ? { ...userMetadata } : {};
+    // ALWAYS add internal namespace with required fields
+    result[BRAINY_NS] = {
+        deleted: false, // CRITICAL: Always false for new items
+        indexed: true, // New items are indexed
+        version: 1, // Current schema version
+        created: now,
+        updated: now
+    };
+    return result;
+}
+/**
+ * Update metadata while preserving namespaces
+ */
+export function updateNamespacedMetadata(existing, updates) {
+    const now = Date.now();
+    // Merge user fields
+    const result = {
+        ...existing,
+        ...updates
+    };
+    // Preserve internal namespace but update timestamp
+    result[BRAINY_NS] = {
+        ...existing[BRAINY_NS],
+        updated: now
+    };
+    // Preserve augmentation namespace
+    if (existing[AUG_NS]) {
+        result[AUG_NS] = existing[AUG_NS];
+    }
+    // Preserve audit trail
+    if (existing[AUDIT_NS]) {
+        result[AUDIT_NS] = existing[AUDIT_NS];
+    }
+    return result;
+}
+/**
+ * Soft delete a noun (O(1) operation)
+ */
+export function markDeleted(metadata) {
+    return {
+        ...metadata,
+        [BRAINY_NS]: {
+            ...metadata[BRAINY_NS],
+            deleted: true,
+            updated: Date.now()
+        }
+    };
+}
+/**
+ * Restore a soft-deleted noun (O(1) operation)
+ */
+export function markRestored(metadata) {
+    return {
+        ...metadata,
+        [BRAINY_NS]: {
+            ...metadata[BRAINY_NS],
+            deleted: false,
+            updated: Date.now()
+        }
+    };
+}
+/**
+ * Check if a noun is deleted (O(1) check)
+ */
+export function isDeleted(metadata) {
+    return metadata[BRAINY_NS]?.deleted === true;
+}
+/**
+ * Get user metadata without internal fields
+ * Used by augmentations to get clean user data
+ */
+export function getUserMetadata(metadata) {
+    const { [BRAINY_NS]: _, [AUG_NS]: __, [AUDIT_NS]: ___, ...userMeta } = metadata;
+    return userMeta;
+}
+/**
+ * Set augmentation data in isolated namespace
+ */
+export function setAugmentationData(metadata, augmentationName, data) {
+    const result = { ...metadata };
+    if (!result[AUG_NS]) {
+        result[AUG_NS] = {};
+    }
+    result[AUG_NS][augmentationName] = data;
+    return result;
+}
+/**
+ * Add audit entry for tracking
+ */
+export function addAuditEntry(metadata, entry) {
+    const result = { ...metadata };
+    if (!result[AUDIT_NS]) {
+        result[AUDIT_NS] = [];
+    }
+    result[AUDIT_NS].push({
+        ...entry,
+        timestamp: Date.now()
+    });
+    return result;
+}
+/**
+ * INDEXING EXPLANATION:
+ *
+ * The MetadataIndex flattens nested objects into dot-notation keys:
+ *
+ * Input metadata:
+ * {
+ *   name: "Django",
+ *   _brainy: {
+ *     deleted: false,
+ *     indexed: true
+ *   }
+ * }
+ *
+ * Creates index entries:
+ * - "name" -> "django" -> Set([id1, id2...])
+ * - "_brainy.deleted" -> "false" -> Set([id1, id2...])  // O(1) lookup!
+ * - "_brainy.indexed" -> "true" -> Set([id1, id2...])
+ *
+ * Query: { "_brainy.deleted": false }
+ * Lookup: index["_brainy.deleted"]["false"] -> Set of IDs in O(1)
+ *
+ * This is why namespacing doesn't hurt performance - it's all flattened!
+ */
+/**
+ * Fields that should ALWAYS be indexed for O(1) access
+ */
+export const ALWAYS_INDEXED_FIELDS = [
+    DELETED_FIELD, // For soft delete filtering
+    INDEXED_FIELD, // For index management
+    VERSION_FIELD // For schema versioning
+];
+/**
+ * Fields that should use sorted index for O(log n) range queries
+ */
+export const SORTED_INDEX_FIELDS = [
+    `${BRAINY_NS}.created`,
+    `${BRAINY_NS}.updated`,
+    `${BRAINY_NS}.priority`,
+    `${BRAINY_NS}.ttl`
+];
+//# sourceMappingURL=metadataNamespace.js.map