feat: harden plugin system wiring and add developer diagnostics

Fix critical wiring bugs that prevented plugin-provided implementations
from being used at runtime. All CRUD operations, fork/checkout/clear,
batch embedding, neural APIs, and VFS path resolution now properly
dispatch through the plugin registry.

Changes:
- Wire graphIndex to storage for getVerbsBySource() fast path
- Replace instanceof checks with duck-typing (indexIsTypeAware flag)
  so plugin HNSW indexes work in add/update/delete/search
- Add createIndex() shared helper for plugin HNSW factory
- Fix fork/checkout/clear to use plugin factories for metadataIndex,
  graphIndex, and HNSW instead of hardcoding JS constructors
- Add three-tier embedBatch priority: embedBatch > embeddings > WASM
- Skip WASM warmup/eagerEmbeddings when plugin provides embeddings
- Fix PathResolver metadataIndex access (was looking on storage)
- Use global UnifiedCache in SemanticPathResolver
- Wire plugin distance function through neural APIs
- Add diagnostics() method and CLI command for provider inspection
- Add requireProviders() for production fail-fast assertions
- Add init-time provider summary log
- Add plugin developer documentation (docs/PLUGINS.md)
- Export DiagnosticsResult type

src/vfs/PathResolver.ts

@@ -201,9 +201,8 @@ export class PathResolver {
    * Falls back to graph traversal if MetadataIndex unavailable
    */
   private async resolveWithMetadataIndex(path: string): Promise<string> {
-    // Access MetadataIndexManager from brain's storage
-    const storage = (this.brain as any).storage
-    const metadataIndex = storage?.metadataIndex
+    // Access MetadataIndexManager from brain instance (not storage — metadataIndex lives on Brainy)
+    const metadataIndex = (this.brain as any).metadataIndex
 
     if (!metadataIndex) {
       // MetadataIndex not available, use graph traversal