I am currently working on a major update to one of my WordPress plugins.
The plugin lets the user choose from several available skins. Quite often I get asked to create a custom skin. To prevent this skin from being deleted on upgrade I have to use a WordPress hook to disable automatic updates for the plugin. This is obviously not ideal as I would want them to still be able to update the plugin. The problem is the way WordPress handles updates - it simply deletes the plugin folder and installs the new version. Thus removing files which were not actually part of the old version.
Currently the only way I can get around it is having two skins folders - one in the plugin folder and one in the uploads folder - is this really the only way I can offer this to my users?