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***Bugsquad note:** This issue has been confirmed several times already. No need to confirm it further.*

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### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Ubuntu 22.04

### Issue description

I followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

I want to create Android launcher app to do this i added following code to AndroidManifest.xml in Android Studio.
`<category android:name="android.intent.category.HOME" />
<category android:name="android.intent.category.DEFAULT" />`

But when I export APK my modifications are removed from AndroidManifest.xml.


### Steps to reproduce

Followed this tutorial
https://docs.godotengine.org/en/stable/tutorials/export/android_custom_build.html#doc-android-custom-build.

then open android project in Android studio and edit AndroidManifest.xml.

### Minimal reproduction project

N/A

if (!DirAccess::exists(p_dir)) {
		Ref<DirAccess> filesystem_da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		ERR_FAIL_COND_V_MSG(filesystem_da.is_null(), ERR_CANT_CREATE, "Cannot create directory '" + p_dir + "'.");
		Error err = filesystem_da->make_dir_recursive(p_dir);
		ERR_FAIL_COND_V_MSG(err, ERR_CANT_CREATE, "Cannot create directory '" + p_dir + "'.");
	}
	return OK;
}
Error store_file_at_path(const String &p_path, const Vector<uint8_t> &p_data) {