refactor(FN-1633): migrate MessageStore from filesystem to SQLite backend

- Replace filesystem-based message storage with SQLite backend
- Add MessageStore class using better-sqlite3 with WAL mode
- Update message.ts CLI command to use new MessageStore API
- Update dashboard routes and engine runtime for SQLite integration
- Update all related tests for new storage implementation

packages/engine/src/runtimes/in-process-runtime.ts

@@ -346,8 +346,7 @@ export class InProcessRuntime
         await this.agentStore.init();
 
         // Initialize MessageStore for wake-on-message behavior
-        this.messageStore = new MessageStoreClass({ rootDir: this.taskStore.getFusionDir() });
-        await this.messageStore.init();
+        this.messageStore = new MessageStoreClass(this.taskStore.getDatabase());
 
         this.heartbeatMonitor = new HeartbeatMonitor({
           store: this.agentStore,