Uploading/creating/removing directories on website
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This is a remote "Red Hat 9.0 Terminal" your using or local on the server hosting the site? If you have FTP access, most update remote sites by those means. Other might use ssh and scp to copy the files over.. more details about your setup always get better responses.
If you are using a kde desktop I can highly recommend KBear for sftp (ssh) and ftp connections. Since it runs in gui on the client system it is very intuitive and easy to use and makes admin of any website/server a breeze.