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/cli/index.ts

@@ -174,6 +174,14 @@ program
   .option('-f, --format <format>', 'Output format (json|csv|jsonl)', 'json')
   .action(coreCommands.export)
 
+program
+  .command('diagnostics')
+  .alias('diag')
+  .description('Show plugin and provider diagnostics')
+  .option('--json', 'Output as JSON')
+  .option('--pretty', 'Pretty print JSON')
+  .action(coreCommands.diagnostics)
+
 // ===== Neural Commands =====
 
 program