fix: avoid double merging of layers

resolves nuxt/framework#3800

Author: pi0

src/loader.ts

@@ -95,27 +95,28 @@ export async function loadConfig<T extends InputConfig=InputConfig> (opts: LoadC
     configRC
   ) as T
 
-  // Preserve unmerged sources
-  const baseLayers = [
-    opts.overrides && { config: opts.overrides, configFile: undefined, cwd: undefined },
-    { config, configFile: opts.configFile, cwd: opts.cwd },
-    opts.rcFile && { config: configRC, configFile: opts.rcFile }
-  ].filter(l => l && l.config)
-
   // Allow extending
   if (opts.extend) {
     await extendConfig(r.config, opts)
-    r.layers = [
-      ...baseLayers,
-      ...r.config._layers
-    ]
+    r.layers = r.config._layers
     delete r.config._layers
     r.config = defu(
       r.config,
       ...r.layers.map(e => e.config)
     ) as T
   }
 
+  // Preserve unmerged sources as layers
+  const baseLayers = [
+    opts.overrides && { config: opts.overrides, configFile: undefined, cwd: undefined },
+    { config, configFile: opts.configFile, cwd: opts.cwd },
+    opts.rcFile && { config: configRC, configFile: opts.rcFile }
+  ].filter(l => l && l.config) as ConfigLayer<T>[]
+  r.layers = [
+    ...baseLayers,
+    ...r.layers
+  ]
+
   // Apply defaults
   if (opts.defaults) {
     r.config = defu(r.config, opts.defaults) as T

test/fixture/base/config.ts

@@ -3,5 +3,6 @@ export default {
   colors: {
     primary: 'base_primary',
     text: 'base_text'
-  }
+  },
+  array: ['b']
 }

test/fixture/config.ts

@@ -7,5 +7,6 @@ export default {
     primary: 'user_primary'
   },
   configFile: true,
-  overriden: false
+  overriden: false,
+  array: ['a']
 }

test/index.test.ts

@@ -27,6 +27,10 @@ describe('c12', () => {
 
     expect(transformPaths(config)).toMatchInlineSnapshot(`
       {
+        "array": [
+          "b",
+          "a",
+        ],
         "baseConfig": true,
         "colors": {
           "primary": "user_primary",
@@ -36,11 +40,6 @@ describe('c12', () => {
         "configFile": true,
         "defaultConfig": true,
         "devConfig": true,
-        "extends": [
-          "./theme",
-          "./config.dev",
-          "virtual",
-        ],
         "overriden": true,
         "rcFile": true,
         "virtual": true,
@@ -59,6 +58,9 @@ describe('c12', () => {
         },
         {
           "config": {
+            "array": [
+              "a",
+            ],
             "colors": {
               "primary": "user_primary",
             },
@@ -90,6 +92,9 @@ describe('c12', () => {
         },
         {
           "config": {
+            "array": [
+              "b",
+            ],
             "baseConfig": true,
             "colors": {
               "primary": "base_primary",