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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

print_line("Installing to device (please wait...): " + devices[p_device].name);
	if (ep.step(TTR("Installing to device, please wait..."), 2)) {
		CLEANUP_AND_RETURN(ERR_SKIP);
	}
	args.clear();
	args.push_back("-s");
	args.push_back(devices[p_device].id);
	args.push_back("install");
	args.push_back("-r");
	args.push_back(tmp_export_path);
	output.clear();
	err = OS::get_singleton()->execute(adb, args, &output, &rv, true);
	print_verbose(output);
	if (err || rv != 0) {
		add_message(EXPORT_MESSAGE_ERROR, TTR("Run"), vformat(TTR("Could not install to device: %s"), output));
		CLEANUP_AND_RETURN(ERR_CANT_CREATE);
	}
	if (use_remote) {
		if (use_reverse) {
			static const char *const msg = "--- Device API >= 21; debugging over USB ---";
			EditorNode::get_singleton()->get_log()->add_message(msg, EditorLog::MSG_TYPE_EDITOR);
			print_line(String(msg).to_upper());
			args.clear();
			args.push_back("-s");
			args.push_back(devices[p_device].id);
			args.push_back("reverse");
			args.push_back("--remove-all");
			output.clear();
			OS::get_singleton()->execute(adb, args, &output, &rv, true);
			print_verbose(output);