Whenever I activate the Clean URL module the hyperlinks in records to linked resources appear to stop working. For example, on the item show page for an item (i.e. myitem1-1) that has as a property for which the value is another resource, it shows property with a link to that other item (i.e. Is Part Of: myitem1). Ordinarily “myitem1” would link to that item, but when I active CleanURL the link breaks, and instead when I hover over it the link shows it trying to go to the same item I am already on (“mysite.com/item/myitem1-1” instead of “mysite.com/item/myitem1”).
The same thing happens in the table where it displays items that link to the item I am currently viewing (so the link to myitem1-1-1 points to myitem1-1, which I am already on instead of myitem1-1-1). Is there some bug in how the Clean URL module is passing URLs for linked resources?
Ok, I found the problem was solved after deactivating the Advanced Search module. However, I create a test installation with a clean new version of Omeka S, and installing those two plugins together didn’t replicate the problem, so it must be something in the way I had Advanced Search configured. Will continue to investigate.
It sounds like the Clean URL module might not be properly handling linked resource paths. You could check if the module has specific settings for linked resources or if there’s a conflict with how URLs are being rewritten. Also, try clearing the cache and re-saving permalink settings.