refactor: migrate from better-sqlite3 to bun:sqlite

- Updated build-hooks.js to remove better-sqlite3 dependency and use bun:sqlite.
- Modified smart-install.js to eliminate checks and installations related to better-sqlite3.
- Refactored Database.ts, SessionSearch.ts, SessionStore.ts, and migrations.ts to import and utilize bun:sqlite.
- Replaced exec and pragma calls with appropriate run methods for bun:sqlite compatibility.
- Removed unnecessary native module verification and installation logic for better-sqlite3.

src/services/sqlite/SessionSearch.ts

@@ -1,4 +1,4 @@
-import Database from 'better-sqlite3';
+import { Database } from 'bun:sqlite';
 import { TableNameRow } from '../../types/database.js';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
 import {
@@ -18,7 +18,7 @@ import {
  * Vector search is handled by ChromaDB - this class only supports filtering without query text
  */
 export class SessionSearch {
-  private db: Database.Database;
+  private db: Database;
 
   constructor(dbPath?: string) {
     if (!dbPath) {
@@ -26,7 +26,7 @@ export class SessionSearch {
       dbPath = DB_PATH;
     }
     this.db = new Database(dbPath);
-    this.db.pragma('journal_mode = WAL');
+    this.db.run('PRAGMA journal_mode = WAL');
 
     // Ensure FTS tables exist
     this.ensureFTSTables();
@@ -60,7 +60,7 @@ export class SessionSearch {
       console.error('[SessionSearch] Creating FTS5 tables...');
 
       // Create observations_fts virtual table
-      this.db.exec(`
+      this.db.run(`
         CREATE VIRTUAL TABLE IF NOT EXISTS observations_fts USING fts5(
           title,
           subtitle,
@@ -74,14 +74,14 @@ export class SessionSearch {
       `);
 
       // Populate with existing data
-      this.db.exec(`
+      this.db.run(`
         INSERT INTO observations_fts(rowid, title, subtitle, narrative, text, facts, concepts)
         SELECT id, title, subtitle, narrative, text, facts, concepts
         FROM observations;
       `);
 
       // Create triggers for observations
-      this.db.exec(`
+      this.db.run(`
         CREATE TRIGGER IF NOT EXISTS observations_ai AFTER INSERT ON observations BEGIN
           INSERT INTO observations_fts(rowid, title, subtitle, narrative, text, facts, concepts)
           VALUES (new.id, new.title, new.subtitle, new.narrative, new.text, new.facts, new.concepts);
@@ -101,7 +101,7 @@ export class SessionSearch {
       `);
 
       // Create session_summaries_fts virtual table
-      this.db.exec(`
+      this.db.run(`
         CREATE VIRTUAL TABLE IF NOT EXISTS session_summaries_fts USING fts5(
           request,
           investigated,
@@ -115,14 +115,14 @@ export class SessionSearch {
       `);
 
       // Populate with existing data
-      this.db.exec(`
+      this.db.run(`
         INSERT INTO session_summaries_fts(rowid, request, investigated, learned, completed, next_steps, notes)
         SELECT id, request, investigated, learned, completed, next_steps, notes
         FROM session_summaries;
       `);
 
       // Create triggers for session_summaries
-      this.db.exec(`
+      this.db.run(`
         CREATE TRIGGER IF NOT EXISTS session_summaries_ai AFTER INSERT ON session_summaries BEGIN
           INSERT INTO session_summaries_fts(rowid, request, investigated, learned, completed, next_steps, notes)
           VALUES (new.id, new.request, new.investigated, new.learned, new.completed, new.next_steps, new.notes);