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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

String dir = p_path.get_base_dir();
	Error err = create_directory(dir);
	if (err != OK) {
		return err;
	}
	Ref<FileAccess> fa = FileAccess::open(p_path, FileAccess::WRITE);
	ERR_FAIL_COND_V_MSG(fa.is_null(), ERR_CANT_CREATE, "Cannot create file '" + p_path + "'.");
	fa->store_buffer(p_data.ptr(), p_data.size());
	return OK;
}
Error store_string_at_path(const String &p_path, const String &p_data) {
	String dir = p_path.get_base_dir();
	Error err = create_directory(dir);
	if (err != OK) {
		if (OS::get_singleton()->is_stdout_verbose()) {
			print_error("Unable to write data into " + p_path);
		}
		return err;
	}
	Ref<FileAccess> fa = FileAccess::open(p_path, FileAccess::WRITE);
	ERR_FAIL_COND_V_MSG(fa.is_null(), ERR_CANT_CREATE, "Cannot create file '" + p_path + "'.");
	fa->store_string(p_data);
	return OK;
}
Error rename_and_store_file_in_gradle_project(void *p_userdata, const String &p_path, const Vector<uint8_t> &p_data, int p_file, int p_total, const Vector<String> &p_enc_in_filters, const Vector<String> &p_enc_ex_filters, const Vector<uint8_t> &p_key) {