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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

Vector<PluginConfigAndroid> enabled_plugins;
	Vector<PluginConfigAndroid> all_plugins = get_plugins();
	for (int i = 0; i < all_plugins.size(); i++) {
		PluginConfigAndroid plugin = all_plugins[i];
		bool enabled = p_presets->get("plugins/" + plugin.name);
		if (enabled) {
			enabled_plugins.push_back(plugin);
		}
	}
	return enabled_plugins;
}
Error EditorExportPlatformAndroid::store_in_apk(APKExportData *ed, const String &p_path, const Vector<uint8_t> &p_data, int compression_method) {
	zip_fileinfo zipfi = get_zip_fileinfo();
	zipOpenNewFileInZip(ed->apk,
			p_path.utf8().get_data(),
			&zipfi,
			nullptr,
			0,
			nullptr,
			0,
			nullptr,
			compression_method,
			Z_DEFAULT_COMPRESSION);
	zipWriteInFileInZip(ed->apk, p_data.ptr(), p_data.size());
	zipCloseFileInZip(ed->apk);
	return OK;
}
Error EditorExportPlatformAndroid::save_apk_so(void *p_userdata, const SharedObject &p_so) {