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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

add_message(EXPORT_MESSAGE_WARNING, TTR("Code Signing"), vformat(TTR("'apksigner' returned with error #%d"), retval));
		add_message(EXPORT_MESSAGE_WARNING, TTR("Code Signing"), vformat(TTR("output: \n%s"), output));
		return ERR_CANT_CREATE;
	}
	if (ep.step(vformat(TTR("Verifying %s..."), export_label), 105)) {
		return ERR_SKIP;
	}
	args.clear();
	args.push_back("verify");
	args.push_back("--verbose");
	args.push_back(export_path);
	if (p_debug) {
		print_verbose("Verifying signed build using: " + String("\n") + apksigner + " " + join_list(args, String(" ")));
	}
	output.clear();
	err = OS::get_singleton()->execute(apksigner, args, &output, &retval, true);
	if (err != OK) {
		add_message(EXPORT_MESSAGE_WARNING, TTR("Code Signing"), TTR("Could not start apksigner executable."));
		return err;
	}
	print_verbose(output);
	if (retval) {
		add_message(EXPORT_MESSAGE_WARNING, TTR("Code Signing"), vformat(TTR("'apksigner' verification of %s failed."), export_label));
		add_message(EXPORT_MESSAGE_WARNING, TTR("Code Signing"), vformat(TTR("output: \n%s"), output));
		return ERR_CANT_CREATE;
	}
	print_verbose("Successfully completed signing build.");
	return OK;
}
void EditorExportPlatformAndroid::_clear_assets_directory() {