There are a couple of tools that can programmatically perform input events. They have some caveats because they work at a lower level so you might need to give them root permissions when that wouldn't have been necessary before, but they do work. The question is if that's all that you were using xdotool for; it's not limited to faking input events. For instance, xdotool can monitor events and trigger actions when you change focus on windows, or specific windows, and it can search across all desktops to find a specific window, bring it to the foreground, resize it, and then feed it input events. If all you need to do is simulate keyboard and mouse events, there are alternatives, but that's not all the tool could do.
This 1,000% for accessibility software or automation frameworks. We don't want a privileged root privileges for emulating mouse/key presses in any application. As a side note Monitoring events might be reasonable, but I wish service could register to monitor without root privileges. Therefore, allowing user discretion.
