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/storage/baseStorage.ts

@@ -379,6 +379,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
     }
   }
 
+  /**
+   * Set the graph index instance (used by Brainy to wire plugin-provided graph indexes).
+   * This ensures getVerbsBySource() uses the fast GraphAdjacencyIndex path
+   * instead of falling back to O(n) shard iteration.
+   */
+  public setGraphIndex(index: GraphAdjacencyIndex): void {
+    this.graphIndex = index
+    this.graphIndexPromise = Promise.resolve(index)
+  }
+
   /**
    * Ensure the storage adapter is initialized
    */