[eluser]Majd Taby[/eluser]
yes, all the URLs to the assets are generated by codex_assets_path, so there's nothing tying your assets folder _inside_ the codex folder. Although I wouldn't recommend having multiple assets folders. The reason being that it makes updating the system harder. Now, in this case, off the top of my head it seems that moving the assets folder outside the application is the only option, but still, something to keep in mind.