What are the potential issues/risks in moving the "css" and "images" folders from the webroot to the assets folder? I understand that the references in the main.php (layout file) need to be updated. But, besides that, can anyone see any reason for NOT doing this?
You can do it, but I recommend to set CAssetManager.basePath and baseUrl to some /assets subdirectory, so you can easily delete all dynamically published assets with one click/command.