Port performance improvements from PR #15

- SQLite performance pragmas: synchronous=NORMAL, 64MB cache,
  memory temp store, 256MB mmap (safe with WAL mode)
- Batch insert for unresolved refs: single transaction instead of
  N individual inserts per file
- Symbol caching (warmCaches): pre-load all nodes into memory maps
  before resolution, eliminating repeated SQLite queries per ref
- Async file I/O: fs.stat/readFile in indexFile() are now non-blocking
- Denormalize filePath/language onto UnresolvedReference: avoids N
  node lookups during resolution, with schema migration v2

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/db/index.ts

@@ -41,6 +41,11 @@ export class DatabaseConnection {
     // Wait up to 2 minutes if database is locked by another process
     // (indexing operations can hold locks for extended periods)
     db.pragma('busy_timeout = 120000');
+    // Performance tuning
+    db.pragma('synchronous = NORMAL');     // Safe with WAL mode
+    db.pragma('cache_size = -64000');      // 64 MB page cache
+    db.pragma('temp_store = MEMORY');      // Temp tables in memory
+    db.pragma('mmap_size = 268435456');    // 256 MB memory-mapped I/O
 
     // Run schema initialization
     const schemaPath = path.join(__dirname, 'schema.sql');
@@ -66,6 +71,11 @@ export class DatabaseConnection {
     // Wait up to 2 minutes if database is locked by another process
     // (indexing operations can hold locks for extended periods)
     db.pragma('busy_timeout = 120000');
+    // Performance tuning
+    db.pragma('synchronous = NORMAL');
+    db.pragma('cache_size = -64000');
+    db.pragma('temp_store = MEMORY');
+    db.pragma('mmap_size = 268435456');
 
     // Check and run migrations if needed
     const conn = new DatabaseConnection(db, dbPath);

src/db/migrations.ts

@@ -9,7 +9,7 @@ import Database from 'better-sqlite3';
 /**
  * Current schema version
  */
-export const CURRENT_SCHEMA_VERSION = 1;
+export const CURRENT_SCHEMA_VERSION = 2;
 
 /**
  * Migration definition
@@ -27,17 +27,16 @@ interface Migration {
  * Future migrations go here.
  */
 const migrations: Migration[] = [
-  // Example migration for version 2 (when needed):
-  // {
-  //   version: 2,
-  //   description: 'Add support for module resolution',
-  //   up: (db) => {
-  //     db.exec(`
-  //       ALTER TABLE nodes ADD COLUMN module_path TEXT;
-  //       CREATE INDEX idx_nodes_module_path ON nodes(module_path);
-  //     `);
-  //   },
-  // },
+  {
+    version: 2,
+    description: 'Add filePath and language to unresolved_refs for performance',
+    up: (db) => {
+      db.exec(`
+        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT;
+        ALTER TABLE unresolved_refs ADD COLUMN language TEXT;
+      `);
+    },
+  },
 ];
 
 /**

src/db/queries.ts

@@ -73,6 +73,8 @@ interface UnresolvedRefRow {
   reference_kind: string;
   line: number;
   col: number;
+  file_path: string | null;
+  language: string | null;
   candidates: string | null;
 }
 
@@ -422,6 +424,14 @@ export class QueryBuilder {
     return rows.map(rowToNode);
   }
 
+  /**
+   * Get all nodes in the database
+   */
+  getAllNodes(): Node[] {
+    const rows = this.db.prepare('SELECT * FROM nodes').all() as NodeRow[];
+    return rows.map(rowToNode);
+  }
+
   /**
    * Search nodes by name using FTS with fallback to LIKE for better matching
    *
@@ -778,8 +788,8 @@ export class QueryBuilder {
   insertUnresolvedRef(ref: UnresolvedReference): void {
     if (!this.stmts.insertUnresolved) {
       this.stmts.insertUnresolved = this.db.prepare(`
-        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, candidates)
-        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @candidates)
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, file_path, language, candidates)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @filePath, @language, @candidates)
       `);
     }
 
@@ -789,10 +799,41 @@ export class QueryBuilder {
       referenceKind: ref.referenceKind,
       line: ref.line,
       col: ref.column,
+      filePath: ref.filePath ?? null,
+      language: ref.language ?? null,
       candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
     });
   }
 
+  /**
+   * Insert multiple unresolved references in a single transaction
+   */
+  insertUnresolvedRefsBatch(refs: UnresolvedReference[]): void {
+    if (refs.length === 0) return;
+
+    if (!this.stmts.insertUnresolved) {
+      this.stmts.insertUnresolved = this.db.prepare(`
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, file_path, language, candidates)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @filePath, @language, @candidates)
+      `);
+    }
+
+    this.db.transaction(() => {
+      for (const ref of refs) {
+        this.stmts.insertUnresolved!.run({
+          fromNodeId: ref.fromNodeId,
+          referenceName: ref.referenceName,
+          referenceKind: ref.referenceKind,
+          line: ref.line,
+          col: ref.column,
+          filePath: ref.filePath ?? null,
+          language: ref.language ?? null,
+          candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
+        });
+      }
+    })();
+  }
+
   /**
    * Delete unresolved references from a node
    */
@@ -821,6 +862,8 @@ export class QueryBuilder {
       referenceKind: row.reference_kind as EdgeKind,
       line: row.line,
       column: row.col,
+      filePath: row.file_path ?? undefined,
+      language: (row.language as Language) ?? undefined,
       candidates: row.candidates ? safeJsonParse<string[]>(row.candidates, []) : undefined,
     }));
   }
@@ -836,6 +879,8 @@ export class QueryBuilder {
       referenceKind: row.reference_kind as EdgeKind,
       line: row.line,
       column: row.col,
+      filePath: row.file_path ?? undefined,
+      language: (row.language as Language) ?? undefined,
       candidates: row.candidates ? safeJsonParse<string[]>(row.candidates, []) : undefined,
     }));
   }

src/db/schema.sql

@@ -11,6 +11,8 @@ CREATE TABLE IF NOT EXISTS schema_versions (
 -- Insert initial version
 INSERT INTO schema_versions (version, applied_at, description)
 VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
+INSERT INTO schema_versions (version, applied_at, description)
+VALUES (2, strftime('%s', 'now') * 1000, 'Add filePath and language to unresolved_refs');
 
 -- =============================================================================
 -- Core Tables
@@ -73,6 +75,8 @@ CREATE TABLE IF NOT EXISTS unresolved_refs (
     reference_kind TEXT NOT NULL,
     line INTEGER NOT NULL,
     col INTEGER NOT NULL,
+    file_path TEXT,
+    language TEXT,
     candidates TEXT, -- JSON array
     FOREIGN KEY (from_node_id) REFERENCES nodes(id) ON DELETE CASCADE
 );