I create a folder/dir and place all my public assets in there for organization and then select those files and folders/dirs to zip/compress.
For example my “organizational” folder/dir contains:
/js
/css
/graphics
config.html
panel.html
where /js, /css, /graphics are folders/dirs containing files or folders/dirs and config.html and panel.html are files.
Also make sure your css and javascript files are not externally linking. That is, copy all your js/css to a file that you will include with your public assets upload.