feat: multi-project engine runtime improvements

- Update project manager and runtime interfaces for multi-project coordination
- Add project engine configuration to core types and settings schema
- Enhance child-process worker tests for signal handling coverage
- Extend in-process runtime with per-project engine lifecycle hooks

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

packages/engine/src/runtimes/child-process-worker.test.ts

@@ -13,13 +13,15 @@ const mockState = vi.hoisted(() => ({
   runtimes: [] as any[],
 }));
 
-vi.mock("../logger.js", () => ({
-  runtimeLog: {
-    log: vi.fn(),
-    warn: vi.fn(),
-    error: vi.fn(),
-  },
-}));
+vi.mock("../logger.js", () => {
+  const mockLogger = { log: vi.fn(), warn: vi.fn(), error: vi.fn() };
+  return {
+    runtimeLog: mockLogger,
+    createLogger: () => mockLogger,
+    schedulerLog: mockLogger,
+    triageLog: mockLogger,
+  };
+});
 
 vi.mock("@fusion/core", () => ({
   CentralCore: class MockCentralCore {},
@@ -88,6 +90,21 @@ vi.mock("./in-process-runtime.js", () => {
   return { InProcessRuntime: MockInProcessRuntime };
 });
 
+vi.mock("../project-engine.js", async () => {
+  const { InProcessRuntime } = await import("./in-process-runtime.js");
+  class MockProjectEngine {
+    private runtime: any;
+    constructor(config: any, centralCore: any, _options?: any) {
+      this.runtime = new InProcessRuntime(config, centralCore);
+    }
+    start = vi.fn(async () => { await this.runtime.start(); });
+    stop = vi.fn(async () => { await this.runtime.stop(); });
+    getRuntime = vi.fn(() => this.runtime);
+    getTaskStore = vi.fn(() => null);
+  }
+  return { ProjectEngine: MockProjectEngine };
+});
+
 type MockWorker = {
   handlers: Map<string, (payload: unknown) => Promise<unknown> | unknown>;
   onCommand: ReturnType<typeof vi.fn>;
@@ -348,7 +365,9 @@ describe("child-process-worker", () => {
       expect(runtime.stop).toHaveBeenCalledTimes(1);
     });
 
-    expect(worker.shutdown).toHaveBeenCalledTimes(1);
+    await vi.waitFor(() => {
+      expect(worker.shutdown).toHaveBeenCalledTimes(1);
+    });
   });
 
   it("SIGINT stops runtime and shuts down IPC worker", async () => {
@@ -363,6 +382,8 @@ describe("child-process-worker", () => {
       expect(runtime.stop).toHaveBeenCalledTimes(1);
     });
 
-    expect(worker.shutdown).toHaveBeenCalledTimes(1);
+    await vi.waitFor(() => {
+      expect(worker.shutdown).toHaveBeenCalledTimes(1);
+    });
   });
 });

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

@@ -89,6 +89,7 @@ export class InProcessRuntime
   private routineRunner?: RoutineRunner;
   private routineScheduler?: RoutineScheduler;
   private missionExecutionLoop?: MissionExecutionLoop;
+  private missionAutopilot?: MissionAutopilot;
   private triageProcessor?: TriageProcessor;
 
   /**
@@ -124,11 +125,16 @@ export class InProcessRuntime
     runtimeLog.log(`Starting InProcessRuntime for project ${this.config.projectId}`);
 
     try {
-      // 1. Initialize TaskStore
+      // 1. Initialize TaskStore (use external if provided, otherwise create new)
       const { TaskStore, PluginStore: PluginStoreClass, PluginLoader: PluginLoaderClass } = await import("@fusion/core");
-      this.taskStore = new TaskStore(this.config.workingDirectory);
-      await this.taskStore.init();
-      runtimeLog.log(`TaskStore initialized for project ${this.config.projectId}`);
+      if (this.config.externalTaskStore) {
+        this.taskStore = this.config.externalTaskStore;
+        runtimeLog.log(`TaskStore provided externally for project ${this.config.projectId}`);
+      } else {
+        this.taskStore = new TaskStore(this.config.workingDirectory);
+        await this.taskStore.init();
+        runtimeLog.log(`TaskStore initialized for project ${this.config.projectId}`);
+      }
 
       // 2. Initialize Plugin system (PluginStore + PluginLoader + PluginRunner)
       this.pluginStore = new PluginStoreClass(this.taskStore.getFusionDir());
@@ -164,15 +170,21 @@ export class InProcessRuntime
         );
       }
 
-      // 4. Initialize global semaphore from CentralCore
-      const globalLimit = await this.getGlobalConcurrencyLimit();
-      this.globalSemaphore = new AgentSemaphore(() => globalLimit);
+      // 4. Initialize global semaphore — use shared one from ProjectManager if provided,
+      // otherwise create a local one from CentralCore (single-project mode).
+      if (this.config.globalSemaphore) {
+        this.globalSemaphore = this.config.globalSemaphore;
+      } else {
+        const globalLimit = await this.getGlobalConcurrencyLimit();
+        this.globalSemaphore = new AgentSemaphore(() => globalLimit);
+      }
 
       // 5. Initialize Scheduler
       const missionStore = this.taskStore.getMissionStore();
-      const missionAutopilot = missionStore
+      this.missionAutopilot = missionStore
         ? new MissionAutopilot(this.taskStore, missionStore)
         : undefined;
+      const missionAutopilot = this.missionAutopilot;
 
       // Initialize MissionExecutionLoop for validation cycle handling
       const missionExecutionLoop = missionStore
@@ -482,6 +494,9 @@ export class InProcessRuntime
         void this.scheduler.reconcileAllMissionFeatures();
       }
 
+      // 14. Start MissionAutopilot background polling
+      this.missionAutopilot?.start();
+
       this.setStatus("active");
       runtimeLog.log(`InProcessRuntime started for project ${this.config.projectId}`);
     } catch (error) {
@@ -563,6 +578,12 @@ export class InProcessRuntime
         runtimeLog.log("Scheduler stopped");
       }
 
+      // 7. Stop mission autopilot background polling
+      if (this.missionAutopilot) {
+        this.missionAutopilot.stop();
+        runtimeLog.log("MissionAutopilot stopped");
+      }
+
       // 7. Stop mission execution loop
       if (this.missionExecutionLoop) {
         this.missionExecutionLoop.stop();
@@ -709,6 +730,22 @@ export class InProcessRuntime
     return this.triageProcessor;
   }
 
+  /**
+   * Get the MissionAutopilot instance (if initialized).
+   * Returns undefined when no MissionStore is available.
+   */
+  getMissionAutopilot(): MissionAutopilot | undefined {
+    return this.missionAutopilot;
+  }
+
+  /**
+   * Get the MissionExecutionLoop instance (if initialized).
+   * Returns undefined when no MissionStore is available.
+   */
+  getMissionExecutionLoop(): MissionExecutionLoop | undefined {
+    return this.missionExecutionLoop;
+  }
+
   /**
    * Execute a heartbeat run for an agent.
    *