Technically, you shouldn't have anything in install/addon because it is supposed to clean up the files after install (but sometimes that might fail).
Anything in install/addon can be removed.
It's possible that one of your add-ons includes a rar and an XML file in the root of the ZIP package. It's preferable that add-on developers put everything they intend to be uploaded into a folder called "upload". The logic my add-on goes through then finds that the easiest way of identifying what should be "uploaded" and what shouldn't.
In the event my add-on can't find an "upload" folder in the ZIP file, it will go through a process to "guess" the correct files to upload.
Alternatively, the add-on developer has decided to put a rar and an XML file in the upload folder in which case that will just get uploaded into root.
If you can identify which add-on it is I can explain in more detail why it's happening, but there's probably not a lot I can do about it.