fix: flush surreal writer after file_metadata persistence

Critical bug: file_metadata was being queued but never flushed to database,
causing project_metadata and file_metadata tables to remain empty.

Root cause: persist_file_metadata() was called after flush_surreal_writer(),
so metadata writes were queued but never persisted before shutdown.

Fix: Added flush_surreal_writer() call after persist_file_metadata() at
line 1237 to ensure all metadata is written to SurrealDB.

This fixes incremental indexing change detection which depends on
file_metadata records.

Author: jruokola

crates/codegraph-mcp/src/indexer.rs

@@ -1234,6 +1234,7 @@ impl ProjectIndexer {
         info!("💾 Updating file metadata for change tracking");
         let file_paths_only: Vec<PathBuf> = files.iter().map(|(p, _)| p.clone()).collect();
         self.persist_file_metadata(&file_paths_only, &nodes, &edges).await?;
+        self.flush_surreal_writer().await?;
 
         // COMPREHENSIVE INDEXING COMPLETION SUMMARY
         info!("🎉 INDEXING COMPLETE - REVOLUTIONARY AI DEVELOPMENT PLATFORM READY!");