Hi,
You can't unfortunatly. Unity 5 has a new way to deal with content imported from a UnityPackage, and so it doesn't recognize existing content on some cases and duplicate newly imported content, so everything renamed is actually newer.
If there is a way around this, I am willing to learn, but from my understanding the best way is to delete the content first and then reimport fresh to avoid renaming and cleaning up manually. PlayMaker package introduced a utility script that runs and clean this up, but it's obviously not practical to do this for every package on the wiki, unfortunatly.
so when I have a folder exposing this problem, I delete the whole folder and re import the package and it works.
MAKE SURE YOU BACKUP WHEN UPGRADING and doing such manipulation.
Bye,
Jean