Hello.
Well that’s a little bit more problematic, because this plugin should care also about theme images and you can select also the plugins folder to optimize everything.
Once you move uploads totally outside of wp-content (which is the only folder that should be changed in WP) then it will be impossible to have this tree-folder-structure selector and it will actually affect a lot of other things.
In case you’re creating some hybrid environment like this and you’re changing the default structure of WP, you will probably need something more than just a simple and free plugin.
As this is a very rare usecase and you’re the first one reporting something like this, I’m afraid I will not solve this soon, because as I wrote above, it will require bigger changes in the plugin. I can not imagine any simple solution right now.
Easiest solution for you would be to write some additional rewrite rule in htaccess, but you will be not able to use this convertor of old images of course.
Maybe when I move this tree-selector one level up, but then it will be confusing for simple users… I’ll think about it, or if you’re developer and have time to do few test and changes, then you can be contributor?
