Keep getting "Command Line Tools for Xcode" Software Update even though I uninstalled

How did you uninstall Xcode? If you just dragged the app to the Trash bin and emptied it there may be other supporting docs left in the system that is triggering the update message.

You can check to see if you've removed all of the supporting files by downloading and running the shareware app Find Any File to search for any files with the application's or the developer's name in the file name.  For Xcode software you'd do the following search(es): 

1 - Name contains xcode

Any files that are found can be dragged from the search results window to the Desktop or Trash bin in the Dock for deletion.

FAF can search areas that Spotlight can't like invisible folders, system folders and packages.  

If you get warnings that the file can't be deleted because it is in use or used by another app boot into Safe Mode according to How to use safe mode on your Mac and delete from there.

Note:  if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode.  This makes it act as a wired keyboard as will assure a successful boot into Safe Mode.

It appears that these might be the ones to remove:

System/Library/CoreServices

System/Library/LaunchAgents

System/Library/LifecyclePolicy

But I'm not sure if those need to be removed. Personally I would reinstall Xcode and use AppCleaner to remove the app and all its supporting files.

WARNING: If you use AppCleaner on an app that you have other apps from the same developer, like Adobe, you must be extremely careful checking all checkboxes and deleting.  Some for those files may support other apps from the same developer and deleting them can mess them up.  Adobe apps is a primary example. I know from experience.  For singular apps from a developer it's safe.

There won't be any problem using AppCleaner on Xcode.

Where were these files located and when did you originally install Xcode, i.e. what system?