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

src/vfs/semantic/SemanticPathResolver.ts

@@ -17,7 +17,7 @@ import { PathResolver } from '../PathResolver.js'
 import { VFSEntity, VFSError, VFSErrorCode } from '../types.js'
 import { SemanticPathParser, ParsedSemanticPath } from './SemanticPathParser.js'
 import { ProjectionRegistry } from './ProjectionRegistry.js'
-import { UnifiedCache } from '../../utils/unifiedCache.js'
+import { getGlobalCache, UnifiedCache } from '../../utils/unifiedCache.js'
 
 /**
  * Semantic Path Resolver
@@ -44,12 +44,8 @@ export class SemanticPathResolver {
     this.registry = registry
     this.parser = new SemanticPathParser()
 
-    // Use Brainy's UnifiedCache for semantic path caching
-    // Zero-config: Uses 2GB default from UnifiedCache
-    this.cache = new UnifiedCache({
-      enableRequestCoalescing: true,
-      enableFairnessCheck: true
-    })
+    // Use global UnifiedCache (picks up plugin-provided cache when available)
+    this.cache = getGlobalCache()
 
     // Create traditional path resolver (uses its own optimized cache with defaults)
     this.pathResolver = new PathResolver(brain, rootEntityId)