is there a way to target themes folder in Bulk Upload? (ex. uploading jquery files/other resources)
Currently there is not. The “Design” tab in CM1 is a pointer to the web_resources directory of the server whereas the bulk uploader moves items into the “Asset” tab which is part of the DB data store and not a file reference.
*If (and only if)* you have server access, you could use a program like WinSCP to transfer lots of files to the web_resources directory. This would accomplish the end result that you’re looking for.
Allowing admins to upload to web_resources would be helpful. Alternately, it would be nice to be able to have an option for “no theme”. In our sites, we typically manage all assets through /Assets/ instead of /web_resources/. If someone accidentally switches the theme for a site, it can cause issues. An option to “select none” for themes would be useful.