feat(vfs): fix VFS visibility by removing broken filtering

- Remove includeVFS parameter and broken isVFS filtering logic
- Add excludeVFS parameter for optional VFS entity filtering
- VFS entities now part of knowledge graph by default
- Enable O(1) graph adjacency optimizations for VFS operations
- Update all VFS projections and PathResolver
- Add comprehensive VFS visibility documentation

This fixes the bug where VFS operations returned empty results due to
operator object mismatch in storage adapters. VFS relationships now use
proper graph traversal without metadata filtering.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/types/brainy.types.ts

@@ -189,7 +189,7 @@ export interface FindParams<T = any> {
   mode?: SearchMode          // Search strategy
   explain?: boolean          // Return scoring explanation
   includeRelations?: boolean // Include entity relationships
-  includeVFS?: boolean       // v4.3.3: Include VFS entities (default: false for knowledge queries)
+  excludeVFS?: boolean       // v4.7.0: Exclude VFS entities from results (default: false - VFS included)
   service?: string           // Multi-tenancy filter
   
   // Triple Intelligence Fusion
@@ -239,7 +239,7 @@ export interface SimilarParams<T = any> {
   type?: NounType | NounType[]    // Restrict to types
   where?: Partial<T>               // Additional filters
   service?: string                 // Multi-tenancy
-  includeVFS?: boolean             // v4.4.0: Include VFS entities (default: false)
+  excludeVFS?: boolean             // v4.7.0: Exclude VFS entities (default: false - VFS included)
 }
 
 /**
@@ -328,17 +328,6 @@ export interface GetRelationsParams {
    * Only return relationships belonging to this service.
    */
   service?: string
-
-  /**
-   * Include VFS relationships (v4.5.1)
-   *
-   * By default, getRelations() excludes VFS relationships (since v4.4.0).
-   * Set this to true when you need to traverse VFS structure.
-   *
-   * @default false
-   * @since v4.5.1
-   */
-  includeVFS?: boolean
 }
 
 // ============= Batch Operations =============