[APM] Fleet support for merging input.config values with other nested properties in the policy input (#101690) (#101955)

* [APM] Improvments in the APM fleet integration (#95501)

* added unit test and line comment

* fixes eslint issues

Co-authored-by: Oliver Gupte <ogupte@users.noreply.github.com>

x-pack/plugins/apm/server/lib/fleet/register_fleet_policy_callbacks.ts

@@ -115,6 +115,7 @@ export function getPackagePolicyWithAgentConfigurations(
       {
         ...firstInput,
         config: {
+          ...firstInput.config,
           [APM_SERVER]: {
             value: {
               ...apmServerValue,

x-pack/plugins/fleet/common/services/package_policies_to_agent_inputs.test.ts

@@ -218,4 +218,81 @@ describe('Fleet - storedPackagePoliciesToAgentInputs', () => {
       },
     ]);
   });
+
+  it('returns agent inputs with deeply merged config values', () => {
+    expect(
+      storedPackagePoliciesToAgentInputs([
+        {
+          ...mockPackagePolicy,
+          inputs: [
+            {
+              ...mockInput,
+              compiled_input: {
+                agent_input_template_group1_vars: {
+                  inputVar: 'input-value',
+                },
+                agent_input_template_group2_vars: {
+                  inputVar3: {
+                    testFieldGroup: {
+                      subField1: 'subfield1',
+                    },
+                    testField: 'test',
+                  },
+                },
+              },
+              config: {
+                agent_input_template_group1_vars: {
+                  value: {
+                    inputVar2: {},
+                  },
+                },
+                agent_input_template_group2_vars: {
+                  value: {
+                    inputVar3: {
+                      testFieldGroup: {
+                        subField2: 'subfield2',
+                      },
+                    },
+                    inputVar4: '',
+                  },
+                },
+              },
+            },
+          ],
+        },
+      ])
+    ).toEqual([
+      {
+        id: 'some-uuid',
+        revision: 1,
+        name: 'mock-package-policy',
+        type: 'test-logs',
+        data_stream: { namespace: 'default' },
+        use_output: 'default',
+        agent_input_template_group1_vars: {
+          inputVar: 'input-value',
+          inputVar2: {},
+        },
+        agent_input_template_group2_vars: {
+          inputVar3: {
+            testField: 'test',
+            testFieldGroup: {
+              subField1: 'subfield1',
+              subField2: 'subfield2',
+            },
+          },
+          inputVar4: '',
+        },
+        streams: [
+          {
+            id: 'test-logs-foo',
+            data_stream: { dataset: 'foo', type: 'logs' },
+            fooKey: 'fooValue1',
+            fooKey2: ['fooValue2'],
+          },
+          { id: 'test-logs-bar', data_stream: { dataset: 'bar', type: 'logs' } },
+        ],
+      },
+    ]);
+  });
 });

x-pack/plugins/fleet/common/services/package_policies_to_agent_inputs.ts

@@ -5,6 +5,8 @@
  * 2.0.
  */
 
+import { merge } from 'lodash';
+
 import type { PackagePolicy, FullAgentPolicyInput, FullAgentPolicyInputStream } from '../types';
 import { DEFAULT_OUTPUT } from '../constants';
 
@@ -31,10 +33,6 @@ export const storedPackagePoliciesToAgentInputs = (
           namespace: packagePolicy.namespace || 'default',
         },
         use_output: DEFAULT_OUTPUT.name,
-        ...Object.entries(input.config || {}).reduce((acc, [key, { value }]) => {
-          acc[key] = value;
-          return acc;
-        }, {} as { [k: string]: any }),
         ...(input.compiled_input || {}),
         ...(input.streams.length
           ? {
@@ -56,6 +54,15 @@ export const storedPackagePoliciesToAgentInputs = (
           : {}),
       };
 
+      // deeply merge the input.config values with the full policy input
+      merge(
+        fullInput,
+        Object.entries(input.config || {}).reduce(
+          (acc, [key, { value }]) => ({ ...acc, [key]: value }),
+          {}
+        )
+      );
+
       if (packagePolicy.package) {
         fullInput.meta = {
           package: {