There have been problems with a missing Plugins.php in the latest
upgrade when done with the upgrade plugin. The upgrade plugin, at least
in some cases, sees this file as deprecated and deletes it.
Most recently this came up with a user upgrading on a mac. I tested it
out on a mac for myself, which is where I noticed the deprecation/delete
message.
https://forum.dokuwiki.org/thread/16642
https://forum.dokuwiki.org/thread/16617