diff --git a/packages/cli/src/commands/onboard/README.md b/packages/cli/src/commands/onboard/README.md
index 71e51a2077..8ab2d5f795 100644
--- a/packages/cli/src/commands/onboard/README.md
+++ b/packages/cli/src/commands/onboard/README.md
@@ -2,22 +2,21 @@
 
 ## Local dev
 
-```bash
-# Checkout the branch
-cd backstage
-git fetch
-git checkout goa/cli-admin-command
-
 # Create a new app
+
+```bash
 cd ..
 npx @backstage/create-app
 cd new-backstage-app
 
 # Run the modded cli in the new app
-../github/backstage/packages/cli/bin/backstage-cli onboard
+
+../RELATIVE_PATH_TO_PROJECT/backstage/packages/cli/bin/backstage-cli onboard
 ? Do you want to set up Authentication for this project? (Y/n)
 ...
 
 # Try the app with the new changes
+
 yarn dev
+
 ```
diff --git a/packages/cli/src/commands/onboard/auth/index.ts b/packages/cli/src/commands/onboard/auth/index.ts
index 5a299e2fb5..0f4537b110 100644
--- a/packages/cli/src/commands/onboard/auth/index.ts
+++ b/packages/cli/src/commands/onboard/auth/index.ts
@@ -16,8 +16,8 @@
 
 import inquirer from 'inquirer';
 import { Task } from '../../../lib/tasks';
-import { github, Answers as GitHubAnswers } from './github';
-import { gitlab, Answers as GitLabAnswers } from './gitlab';
+import { github, Answers as GitHubAnswers } from './providers/github';
+import { gitlab, Answers as GitLabAnswers } from './providers/gitlab';
 
 export { type GitHubAnswers, type GitLabAnswers };
 
diff --git a/packages/cli/src/commands/onboard/auth/github/index.ts b/packages/cli/src/commands/onboard/auth/providers/github.ts
similarity index 100%
rename from packages/cli/src/commands/onboard/auth/github/index.ts
rename to packages/cli/src/commands/onboard/auth/providers/github.ts
diff --git a/packages/cli/src/commands/onboard/auth/gitlab/index.ts b/packages/cli/src/commands/onboard/auth/providers/gitlab.ts
similarity index 100%
rename from packages/cli/src/commands/onboard/auth/gitlab/index.ts
rename to packages/cli/src/commands/onboard/auth/providers/gitlab.ts
diff --git a/packages/cli/src/commands/onboard/config.ts b/packages/cli/src/commands/onboard/config.ts
index 8d419dd71a..cce3119fcc 100644
--- a/packages/cli/src/commands/onboard/config.ts
+++ b/packages/cli/src/commands/onboard/config.ts
@@ -22,15 +22,24 @@ const readYaml = async (file: string) => {
 };
 
 export const updateConfigFile = async <T>(file: string, config: T) => {
-  const content = fs.existsSync(file)
-    ? { ...(await readYaml(file)), ...config }
-    : { ...config };
+  const staticContent =
+    '# Backstage override configuration for your local development environment \n';
 
-  return await fs.writeFile(
-    file,
-    yaml.stringify(content, {
-      indent: 2,
-    }),
-    'utf8',
-  );
+  const content = fs.existsSync(file)
+    ? yaml.stringify(
+        { ...(await readYaml(file)), ...config },
+        {
+          indent: 2,
+        },
+      )
+    : staticContent.concat(
+        yaml.stringify(
+          { ...config },
+          {
+            indent: 2,
+          },
+        ),
+      );
+
+  return await fs.writeFile(file, content, 'utf8');
 };
diff --git a/packages/cli/src/commands/onboard/integrations/github/index.ts b/packages/cli/src/commands/onboard/integrations/github.ts
similarity index 95%
rename from packages/cli/src/commands/onboard/integrations/github/index.ts
rename to packages/cli/src/commands/onboard/integrations/github.ts
index 883a119c00..a0538c7ace 100644
--- a/packages/cli/src/commands/onboard/integrations/github/index.ts
+++ b/packages/cli/src/commands/onboard/integrations/github.ts
@@ -16,10 +16,10 @@
 
 import chalk from 'chalk';
 import inquirer from 'inquirer';
-import { Task } from '../../../../lib/tasks';
-import { updateConfigFile } from '../../config';
-import { APP_CONFIG_FILE } from '../../files';
-import { GitHubAnswers } from '../../auth';
+import { Task } from '../../../lib/tasks';
+import { updateConfigFile } from '../config';
+import { APP_CONFIG_FILE } from '../files';
+import { GitHubAnswers } from '../auth';
 
 type Answers = {
   hasEnterprise: boolean;