deepmerge in merging apm-configuration (#179048)

We faced an issue where APM global labels sourced from the kibana
configuration were overriden when `ELASTIC_APM_GLOBAL_LABELS` was set in
the run-time.

I suspect this is due to the fact hat the use a shallow merge at this
point,
and the labels are nested inside both configuration (
`configFromKibanaConfig`, and `configFromEnv` ).
```
config =  Object {
         ...
         "globalLabels": Object {
                ....
         },
         ...
}
```

Didn't set up my IDE to actually test this. But added a unit test which
will hopefully give some feedback

---------

Co-authored-by: Jean-Louis Leysens <jloleysens@gmail.com>

packages/kbn-apm-config-loader/src/config.test.ts

@@ -7,9 +7,9 @@
  */
 import type { AgentConfigOptions, Labels } from 'elastic-apm-node';
 import {
-  packageMock,
-  mockedRootDir,
   gitRevExecMock,
+  mockedRootDir,
+  packageMock,
   readUuidFileMock,
   resetAllMocks,
 } from './config.test.mocks';
@@ -152,6 +152,7 @@ describe('ApmConfiguration', () => {
       delete process.env.ELASTIC_APM_SECRET_TOKEN;
       delete process.env.ELASTIC_APM_API_KEY;
       delete process.env.ELASTIC_APM_SERVER_URL;
+      delete process.env.ELASTIC_APM_GLOBAL_LABELS;
       delete process.env.NODE_ENV;
     });
 
@@ -184,6 +185,21 @@ describe('ApmConfiguration', () => {
           })
         );
       });
+
+      it('ELASTIC_APM_GLOBAL_LABELS', () => {
+        process.env.ELASTIC_APM_GLOBAL_LABELS = 'test1=1,test2=2';
+        const config = new ApmConfiguration(mockedRootDir, {}, true);
+
+        expect(config.getConfig('serviceName')).toEqual(
+          expect.objectContaining({
+            globalLabels: {
+              git_rev: 'sha',
+              test1: '1',
+              test2: '2',
+            },
+          })
+        );
+      });
     });
 
     it('does not override the environment from NODE_ENV if already set in the config file', () => {

packages/kbn-apm-config-loader/src/config.ts

@@ -7,6 +7,7 @@
  */
 
 import { join } from 'path';
+import deepmerge from 'deepmerge';
 import { merge } from 'lodash';
 import { execSync } from 'child_process';
 import { getDataPath } from '@kbn/utils';
@@ -295,7 +296,10 @@ export class ApmConfiguration {
     const { servicesOverrides, redactUsers, ...configFromKibanaConfig } =
       this.getConfigFromKibanaConfig();
     const configFromEnv = this.getConfigFromEnv(configFromKibanaConfig);
-    const config = merge({}, configFromKibanaConfig, configFromEnv);
+    const config = [configFromKibanaConfig, configFromEnv].reduce<AgentConfigOptions>(
+      (acc, conf) => deepmerge(acc, conf),
+      {}
+    );
 
     if (config.active === false && config.contextPropagationOnly !== false) {
       throw new Error(