[Ops] Change dev-cli's config merging logic (#163928)

## Summary
Change config merging behaviour, so that arrays are not
merged/concatenated but replaced.

Closes: #162842 

Related to: https://github.com/elastic/kibana/pull/161884

Co-authored-by: Kibana Machine <42973632+kibanamachine@users.noreply.github.com>

src/cli/serve/serve.js

@@ -55,11 +55,11 @@ function pathCollector() {
 const configPathCollector = pathCollector();
 const pluginPathCollector = pathCollector();
 
-function applyConfigOverrides(rawConfig, opts, extraCliOptions) {
+export function applyConfigOverrides(rawConfig, opts, extraCliOptions) {
   const set = _.partial(lodashSet, rawConfig);
   const get = _.partial(_.get, rawConfig);
   const has = _.partial(_.has, rawConfig);
-  const merge = _.partial(_.merge, rawConfig);
+
   if (opts.oss) {
     delete rawConfig.xpack;
   }
@@ -135,8 +135,8 @@ function applyConfigOverrides(rawConfig, opts, extraCliOptions) {
 
   set('plugins.paths', _.compact([].concat(get('plugins.paths'), opts.pluginPath)));
 
-  merge(extraCliOptions);
-  merge(readKeystore());
+  _.mergeWith(rawConfig, extraCliOptions, mergeAndReplaceArrays);
+  _.merge(rawConfig, readKeystore());
 
   return rawConfig;
 }
@@ -257,3 +257,15 @@ export default function (program) {
     });
   });
 }
+
+function mergeAndReplaceArrays(objValue, srcValue) {
+  if (typeof srcValue === 'undefined') {
+    return objValue;
+  } else if (Array.isArray(srcValue)) {
+    // do not merge arrays, use new value instead
+    return srcValue;
+  } else {
+    // default to default merging
+    return undefined;
+  }
+}

src/cli/serve/serve.test.js

@@ -0,0 +1,81 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License
+ * 2.0 and the Server Side Public License, v 1; you may not use this file except
+ * in compliance with, at your election, the Elastic License 2.0 or the Server
+ * Side Public License, v 1.
+ */
+
+import { applyConfigOverrides } from './serve';
+
+describe('applyConfigOverrides', () => {
+  it('merges empty objects to an empty config', () => {
+    const output = applyConfigOverrides({}, {}, {});
+    const defaultEmptyConfig = {
+      plugins: {
+        paths: [],
+      },
+    };
+
+    expect(output).toEqual(defaultEmptyConfig);
+  });
+
+  it('merges objects', () => {
+    const output = applyConfigOverrides(
+      {
+        tomato: {
+          size: 40,
+          color: 'red',
+        },
+      },
+      {},
+      {
+        tomato: {
+          weight: 100,
+        },
+      }
+    );
+
+    expect(output).toEqual({
+      tomato: {
+        weight: 100,
+        color: 'red',
+        size: 40,
+      },
+      plugins: {
+        paths: [],
+      },
+    });
+  });
+
+  it('merges objects, but not arrays', () => {
+    const output = applyConfigOverrides(
+      {
+        tomato: {
+          color: 'red',
+          arr: [1, 2, 3],
+        },
+      },
+      {},
+      {
+        xyz: 40,
+        tomato: {
+          weight: 100,
+          arr: [4, 5],
+        },
+      }
+    );
+
+    expect(output).toEqual({
+      xyz: 40,
+      tomato: {
+        weight: 100,
+        color: 'red',
+        arr: [4, 5],
+      },
+      plugins: {
+        paths: [],
+      },
+    });
+  });
+});