fix: set verb.source/target to entity UUID instead of NounType

relate() was setting verb.source = fromEntity.type (a NounType like
"concept") instead of the entity UUID. Cortex's graph index indexes by
verb.source, so lookups by UUID found nothing — causing in-session
reads to return 0 results.

Also fixes:
- PathResolver calling private getIdsFromChunks() → public getIds()
- Plugin auto-detection removed; cortex loads only via explicit config
- GraphVerb types accept number timestamps and sourceId/targetId aliases
- Dead autoDetect() method removed from PluginRegistry
- In-session regression tests added for getRelations after relate()

src/brainy.ts

@@ -1488,14 +1488,14 @@ export class Brainy<T = any> implements BrainyInterface<T> {
         vector: relationVector,
         sourceId: params.from,
         targetId: params.to,
-        source: fromEntity.type,
-        target: toEntity.type,
+        source: params.from,
+        target: params.to,
         verb: params.type,
         type: params.type,
         weight: params.weight ?? 1.0,
-        metadata: params.metadata as any,
+        metadata: params.metadata,
         createdAt: Date.now()
-      } as any
+      }
 
       // Execute atomically with transaction system
       await this.transactionManager.executeTransaction(async (tx) => {
@@ -6694,15 +6694,14 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    */
   private async loadPlugins(): Promise<void> {
     // plugins config:
-    //   undefined (default) → auto-detect installed plugins
-    //   false               → no plugins, skip auto-detection
-    //   []                  → no plugins, skip auto-detection
-    //   ['@soulcraft/cortex'] → load only these, no auto-detection
+    //   undefined (default) → no auto-detection (safe default)
+    //   false               → no auto-detection
+    //   []                  → no auto-detection
+    //   ['@soulcraft/cortex'] → load only these explicitly listed packages
+    // Note: plugins registered via brain.use() are always activated regardless of config
     const pluginConfig = this.config.plugins
-    if (pluginConfig === false) {
-      // Explicitly disabled — no plugins
-    } else if (Array.isArray(pluginConfig)) {
-      // Explicit list: only register the specified packages, no auto-detection
+    if (Array.isArray(pluginConfig) && pluginConfig.length > 0) {
+      // Explicit list: import and register the specified packages
       for (const pkg of pluginConfig) {
         try {
           const mod = await import(pkg)
@@ -6714,9 +6713,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
           // Package not found — skip
         }
       }
-    } else {
-      // Default: auto-detect known plugins
-      await this.pluginRegistry.autoDetect()
     }
 
     // Create plugin context

src/coreTypes.ts

@@ -291,15 +291,15 @@ export interface GraphVerb {
   service?: string // Multi-tenancy support - which service created this verb
 
   // Additional properties used in the codebase
-  source?: string // Alias for sourceId
-  target?: string // Alias for targetId
+  source?: string // Entity UUID (same as sourceId, for graphTypes compatibility)
+  target?: string // Entity UUID (same as targetId, for graphTypes compatibility)
   verb?: string // Alias for type
   data?: Record<string, any> // Additional flexible data storage
   embedding?: Vector // Alias for vector
 
   // Timestamp and creator properties
-  createdAt?: { seconds: number; nanoseconds: number } // When the verb was created
-  updatedAt?: { seconds: number; nanoseconds: number } // When the verb was last updated
+  createdAt?: number | { seconds: number; nanoseconds: number } // When the verb was created
+  updatedAt?: number | { seconds: number; nanoseconds: number } // When the verb was last updated
   createdBy?: { augmentation: string; version: string } // Information about what created this verb
 }
 

src/plugin.ts

@@ -84,29 +84,6 @@ export class PluginRegistry {
     this.plugins.set(plugin.name, plugin)
   }
 
-  /**
-   * Auto-detect known plugins by attempting dynamic import.
-   * Additional package names can be passed for third-party plugins.
-   */
-  async autoDetect(additionalPackages: string[] = []): Promise<void> {
-    const packages = [
-      '@soulcraft/cortex',
-      '@soulcraft/brainy-cortex',  // deprecated — backward compat
-      ...additionalPackages
-    ]
-
-    for (const pkg of packages) {
-      try {
-        const mod = await import(pkg)
-        const plugin: BrainyPlugin = mod.default || mod
-        if (plugin && typeof plugin.activate === 'function' && plugin.name) {
-          this.plugins.set(plugin.name, plugin)
-        }
-      } catch {
-        // Package not installed — skip silently
-      }
-    }
-  }
 
   /**
    * Activate all registered plugins.

src/types/graphTypes.ts

@@ -369,12 +369,14 @@ export interface GraphNoun {
  */
 export interface GraphVerb {
   id: string // Unique identifier for the verb
-  source: string // ID of the source noun
-  target: string // ID of the target noun
+  source: string // Entity UUID of the source noun
+  target: string // Entity UUID of the target noun
+  sourceId?: string // Alias for source (coreTypes compatibility)
+  targetId?: string // Alias for target (coreTypes compatibility)
   label?: string // Optional descriptive label
   verb: VerbType // Type of relationship
-  createdAt: Timestamp // When the verb was created
-  updatedAt: Timestamp // When the verb was last updated
+  createdAt: Timestamp | number // When the verb was created
+  updatedAt: Timestamp | number // When the verb was last updated
   createdBy: CreatorMetadata // Information about what created this verb
   service?: string // Multi-tenancy support - which service created this verb
   data?: Record<string, any> // Additional flexible data storage

src/vfs/PathResolver.ts

@@ -214,7 +214,7 @@ export class PathResolver {
     try {
       // Direct O(log n) query to roaring bitmap index
       // This queries the 'path' field in VFS entity metadata
-      const ids = await metadataIndex.getIdsFromChunks('path', path)
+      const ids = await metadataIndex.getIds('path', path)
 
       if (ids.length === 0) {
         this.metadataIndexMisses++

tests/unit/vfs-restart-fix.test.ts

@@ -33,13 +33,17 @@ describe('VFS restart persistence', () => {
       entityId = await brain.vfs.resolvePathToId('/chapter-1.txt')
       expect(entityId).toBeTruthy()
 
-      // Verify within same session
+      // Verify within same session — entity, readdir, and relations
       const entity1 = await brain.get(entityId!)
       expect(entity1).not.toBeNull()
 
       const entries1 = await brain.vfs.readdir('/')
       expect(entries1.length).toBeGreaterThan(0)
 
+      // In-session getRelations: root should have Contains relationship to the file
+      const relations1 = await brain.getRelations({ from: rootId, type: VerbType.Contains })
+      expect(relations1.length).toBeGreaterThan(0)
+
       await brain.close()
 
       // === SESSION 2: Read data after restart ===
@@ -100,6 +104,10 @@ describe('VFS restart persistence', () => {
       const docEntries1 = await brain.vfs.readdir('/docs')
       expect(docEntries1.length).toBe(2) // guide.txt + api.txt
 
+      // In-session getRelations: root should have Contains relationships
+      const rootRelations1 = await brain.getRelations({ from: rootId, type: VerbType.Contains })
+      expect(rootRelations1.length).toBeGreaterThan(0)
+
       await brain.close()
 
       // === SESSION 2: Verify all data persisted ===