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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 fullpath = get_apk_expansion_fullpath(p_preset, p_path);
	Error err = save_pack(p_preset, p_debug, fullpath);
	return err;
}
void EditorExportPlatformAndroid::get_command_line_flags(const Ref<EditorExportPreset> &p_preset, const String &p_path, int p_flags, Vector<uint8_t> &r_command_line_flags) {
	String cmdline = p_preset->get("command_line/extra_args");
	Vector<String> command_line_strings = cmdline.strip_edges().split(" ");
	for (int i = 0; i < command_line_strings.size(); i++) {
		if (command_line_strings[i].strip_edges().length() == 0) {
			command_line_strings.remove_at(i);
			i--;
		}
	}
	gen_export_flags(command_line_strings, p_flags);
	bool apk_expansion = p_preset->get("apk_expansion/enable");
	if (apk_expansion) {
		String fullpath = get_apk_expansion_fullpath(p_preset, p_path);
		String apk_expansion_public_key = p_preset->get("apk_expansion/public_key");
		command_line_strings.push_back("--use_apk_expansion");
		command_line_strings.push_back("--apk_expansion_md5");
		command_line_strings.push_back(FileAccess::get_md5(fullpath));
		command_line_strings.push_back("--apk_expansion_key");
		command_line_strings.push_back(apk_expansion_public_key.strip_edges());
	}
	int xr_mode_index = p_preset->get("xr_features/xr_mode");
	if (xr_mode_index == XR_MODE_OPENXR) {