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/cli/commands/core.ts

@@ -347,10 +347,8 @@ export const coreCommands = {
         searchParams.includeRelations = true
       }
 
-      // Include VFS files (v4.4.0 - find excludes VFS by default)
-      if (options.includeVfs) {
-        searchParams.includeVFS = true
-      }
+      // v4.7.0: VFS is now part of the knowledge graph (included by default)
+      // Users can exclude VFS with --where vfsType exists:false if needed
 
       // Triple Intelligence Fusion - custom weighting
       if (options.fusion || options.vectorWeight || options.graphWeight || options.fieldWeight) {