In reply to alex.

alex:

First, if you follow the instructions for a manual update properly, as given here: https://codex.wordpress.org/Updating_WordPress#Manual_Update , then you might notice step 4 has the word "Delete" in it.

Secondly, theme and plugin updates performed through the one-click process do indeed "clean up", because they delete the entire theme or plugin directory during that process, and replace it.

Simply overwriting files and leaving old ones around is not a proper way to do an upgrade, and it's not the way done by WordPress itself or the way given in our instructions.