Turn on deprecation logs in Jest integration tests (#199095)

## Summary

Part of preparing for 9.0 release we monitor test logs to surface
deprecated ES usage in Kibana. This PR ensures that all Jest integration
test are surfacing these logs by default.

packages/core/test-helpers/core-test-helpers-kbn-server/src/create_root.ts

@@ -43,6 +43,22 @@ const DEFAULTS_SETTINGS = {
     root: {
       level: 'off',
     },
+    loggers: [
+      {
+        name: 'root',
+        level: 'error',
+        appenders: ['console'],
+      },
+      {
+        name: 'elasticsearch.deprecation',
+        level: 'all',
+        appenders: ['deprecation'],
+      },
+    ],
+    appenders: {
+      deprecation: { type: 'console', layout: { type: 'json' } },
+      console: { type: 'console', layout: { type: 'pattern' } },
+    },
   },
   plugins: {},
   migrations: { skip: false },

src/core/server/integration_tests/http/logging.test.ts

@@ -28,11 +28,28 @@ describe('request logging', () => {
 
   describe('http server response logging', () => {
     describe('configuration', () => {
+      let root: ReturnType<typeof createRoot>;
+
+      afterEach(async () => {
+        await root?.shutdown();
+      });
       it('does not log with a default config', async () => {
-        const root = createRoot({
+        root = createRoot({
           plugins: { initialize: false },
           elasticsearch: { skipStartupConnectionCheck: true },
           server: { restrictInternalApis: false },
+          logging: {
+            appenders: {
+              'test-console': { type: 'console', layout: { type: 'json' } },
+            },
+            loggers: [
+              {
+                name: 'http.server.response',
+                appenders: ['test-console'],
+                level: 'off',
+              },
+            ],
+          },
         });
         await root.preboot();
         const { http } = await root.setup();
@@ -47,12 +64,10 @@ describe('request logging', () => {
 
         await request.get(root, '/ping').expect(200, 'pong');
         expect(mockConsoleLog).not.toHaveBeenCalled();
-
-        await root.shutdown();
       });
 
       it('logs at the correct level and with the correct context', async () => {
-        const root = createRoot({
+        root = createRoot({
           logging: {
             appenders: {
               'test-console': {
@@ -93,8 +108,6 @@ describe('request logging', () => {
         const [level, logger] = mockConsoleLog.mock.calls[0][0].split('|');
         expect(level).toBe('DEBUG');
         expect(logger).toBe('http.server.response');
-
-        await root.shutdown();
       });
     });
 
@@ -131,7 +144,7 @@ describe('request logging', () => {
       });
 
       afterEach(async () => {
-        await root.shutdown();
+        await root?.shutdown();
       });
 
       it('handles a GET request', async () => {

src/core/server/integration_tests/node/logging.test.ts

@@ -16,6 +16,13 @@ function createRootWithRoles(roles: string[]) {
       roles,
     },
     logging: {
+      loggers: [
+        {
+          name: 'root',
+          appenders: ['test-console'],
+          level: 'info',
+        },
+      ],
       appenders: {
         'test-console': {
           type: 'console',