Refactor code structure for improved readability and maintainability

Author: hotlong

examples/app-host/src/index.ts

@@ -1,4 +1,4 @@
-import { ObjectKernel, DriverPlugin, AppPlugin } from '@objectstack/runtime';
+import { ObjectKernel, DriverPlugin, AppPlugin, createApiRegistryPlugin } from '@objectstack/runtime';
 import { InMemoryDriver } from '@objectstack/driver-memory';
 import { ObjectQLPlugin } from '@objectstack/objectql';
 import { HonoServerPlugin } from '@objectstack/plugin-hono-server';
@@ -30,6 +30,9 @@ import BiPluginManifest from '@example/plugin-bi/objectstack.config';
   await kernel.use(new AppPlugin(TodoApp));
   await kernel.use(new AppPlugin(BiPluginManifest));
 
+  // Register API Registry (Required for Hono Server)
+  await kernel.use(createApiRegistryPlugin());
+
   // Load the Hono Server Plugin
   await kernel.use(new HonoServerPlugin({ 
     port: 3004, 

packages/core/src/api-registry.test.ts

@@ -657,8 +657,8 @@ describe('ApiRegistry', () => {
       });
 
       const snapshot = registry.getRegistry();
-      expect(snapshot.byType?.rest.length).toBe(2);
-      expect(snapshot.byType?.graphql.length).toBe(1);
+      expect(snapshot.byType?.rest?.length).toBe(2);
+      expect(snapshot.byType?.graphql?.length).toBe(1);
     });
   });
 

packages/core/src/dependency-resolver.ts

@@ -3,7 +3,7 @@ import type {
   VersionConstraint,
   CompatibilityLevel,
   DependencyConflict
-} from '@objectstack/spec/system';
+} from '@objectstack/spec/kernel';
 import type { ObjectLogger } from './logger.js';
 
 /**

packages/core/src/health-monitor.test.ts

@@ -1,7 +1,7 @@
 import { describe, it, expect, beforeEach } from 'vitest';
 import { PluginHealthMonitor } from './health-monitor.js';
 import { createLogger } from './logger.js';
-import type { PluginHealthCheck } from '@objectstack/spec/system';
+import type { PluginHealthCheck } from '@objectstack/spec/kernel';
 
 describe('PluginHealthMonitor', () => {
   let monitor: PluginHealthMonitor;

packages/core/src/health-monitor.ts

@@ -2,7 +2,7 @@ import type {
   PluginHealthStatus, 
   PluginHealthCheck, 
   PluginHealthReport 
-} from '@objectstack/spec/system';
+} from '@objectstack/spec/kernel';
 import type { ObjectLogger } from './logger.js';
 import type { Plugin } from './types.js';
 

packages/core/src/hot-reload.ts

@@ -1,7 +1,7 @@
 import type { 
   HotReloadConfig, 
   PluginStateSnapshot 
-} from '@objectstack/spec/system';
+} from '@objectstack/spec/kernel';
 import type { ObjectLogger } from './logger.js';
 import type { Plugin } from './types.js';
 

packages/core/src/security/permission-manager.test.ts

@@ -1,7 +1,7 @@
 import { describe, it, expect, beforeEach } from 'vitest';
 import { PluginPermissionManager } from './permission-manager.js';
 import { createLogger } from '../logger.js';
-import type { PermissionSet } from '@objectstack/spec/system';
+import type { PermissionSet } from '@objectstack/spec/kernel';
 
 describe('PluginPermissionManager', () => {
   let manager: PluginPermissionManager;

packages/core/src/security/permission-manager.ts

@@ -3,7 +3,7 @@ import type {
   PermissionSet,
   PermissionAction,
   ResourceType
-} from '@objectstack/spec/system';
+} from '@objectstack/spec/kernel';
 import type { ObjectLogger } from '../logger.js';
 
 /**

packages/core/src/security/plugin-permission-enforcer.test.ts

@@ -1,7 +1,7 @@
 import { describe, it, expect, beforeEach } from 'vitest';
 import { PluginPermissionEnforcer, SecurePluginContext } from './plugin-permission-enforcer.js';
 import { createLogger } from '../logger.js';
-import type { PluginCapability } from '@objectstack/spec/system';
+import type { PluginCapability } from '@objectstack/spec/kernel';
 import type { PluginContext } from '../types.js';
 
 describe('PluginPermissionEnforcer', () => {

packages/core/src/security/plugin-permission-enforcer.ts

@@ -1,5 +1,5 @@
 import type { Logger } from '@objectstack/spec/contracts';
-import type { PluginCapability } from '@objectstack/spec/system';
+import type { PluginCapability } from '@objectstack/spec/kernel';
 import type { PluginContext } from '../types.js';
 
 /**