fix: checkpoint WAL before database backup to prevent data loss

fs.copyFileSync on a WAL-mode SQLite database can produce incomplete
backups because committed data may still reside in the -wal file.
Added safeBackupCopy() that runs PRAGMA wal_checkpoint(TRUNCATE) before
copying, ensuring the .db file is self-contained.

src/__tests__/main/stats/stats-db.test.ts

@@ -851,6 +851,60 @@ describe('Daily backup system', () => {
 			expect(dailyBackupCalls).toHaveLength(0);
 		});
 	});
+
+	describe('WAL checkpoint before backup', () => {
+		it('should checkpoint WAL before creating daily backup', async () => {
+			const today = new Date().toISOString().split('T')[0];
+			mockFsExistsSync.mockImplementation((p: unknown) => {
+				if (typeof p === 'string' && p.includes(`daily.${today}`)) return false;
+				return true;
+			});
+
+			const { StatsDB } = await import('../../../main/stats');
+			const db = new StatsDB();
+			db.initialize();
+
+			// Should have called wal_checkpoint(TRUNCATE) before copyFileSync
+			expect(mockDb.pragma).toHaveBeenCalledWith('wal_checkpoint(TRUNCATE)');
+		});
+
+		it('should checkpoint WAL before creating manual backup', async () => {
+			const { StatsDB } = await import('../../../main/stats');
+			const db = new StatsDB();
+			db.initialize();
+
+			mockDb.pragma.mockClear();
+			db.backupDatabase();
+
+			expect(mockDb.pragma).toHaveBeenCalledWith('wal_checkpoint(TRUNCATE)');
+		});
+
+		it('should call checkpoint before copyFileSync (correct ordering)', async () => {
+			const callOrder: string[] = [];
+			mockDb.pragma.mockImplementation((pragmaStr: string) => {
+				if (pragmaStr === 'wal_checkpoint(TRUNCATE)') {
+					callOrder.push('checkpoint');
+				}
+				if (pragmaStr === 'integrity_check') return [{ integrity_check: 'ok' }];
+				return [{ user_version: 3 }];
+			});
+			mockFsCopyFileSync.mockImplementation(() => {
+				callOrder.push('copy');
+			});
+
+			const { StatsDB } = await import('../../../main/stats');
+			const db = new StatsDB();
+			db.initialize();
+
+			mockDb.pragma.mockClear();
+			mockFsCopyFileSync.mockClear();
+			callOrder.length = 0;
+
+			db.backupDatabase();
+
+			expect(callOrder).toEqual(['checkpoint', 'copy']);
+		});
+	});
 });
 
 /**

src/main/stats/stats-db.ts

@@ -321,6 +321,22 @@ export class StatsDB {
 		}
 	}
 
+	/**
+	 * Checkpoint WAL to flush pending writes into the main database file,
+	 * then copy the database file to the destination path.
+	 *
+	 * Plain fs.copyFileSync on a WAL-mode database can produce an incomplete
+	 * copy because committed data may still reside in the -wal file.
+	 * PRAGMA wal_checkpoint(TRUNCATE) forces all WAL content into the main
+	 * file and resets the WAL, making the .db file self-contained.
+	 */
+	private safeBackupCopy(destPath: string): void {
+		if (this.db) {
+			this.db.pragma('wal_checkpoint(TRUNCATE)');
+		}
+		fs.copyFileSync(this.dbPath, destPath);
+	}
+
 	/**
 	 * Create a backup of the current database file.
 	 */
@@ -333,7 +349,7 @@ export class StatsDB {
 			const timestamp = Date.now();
 			const backupPath = `${this.dbPath}.backup.${timestamp}`;
 
-			fs.copyFileSync(this.dbPath, backupPath);
+			this.safeBackupCopy(backupPath);
 
 			logger.info(`Created database backup at ${backupPath}`, LOG_CONTEXT);
 			return { success: true, backupPath };
@@ -367,8 +383,8 @@ export class StatsDB {
 				return;
 			}
 
-			// Create today's backup
-			fs.copyFileSync(this.dbPath, dailyBackupPath);
+			// Create today's backup (checkpoint WAL first so the copy is self-contained)
+			this.safeBackupCopy(dailyBackupPath);
 			logger.info(`Created daily backup: ${dailyBackupPath}`, LOG_CONTEXT);
 
 			// Rotate old backups (keep last 7 days)