John,
As mentioned by others, there are better ways to use FTP/Editors than the manual method you are using. The real trick here is to avoid using the HCI GUI Script Editor all together. The main reason is syntax highlighting which helps to reduce coding bugs and errors while speeding up code development.
The GUI Editor is a last resort tool that is only in the Cloverleaf GUI “for completeness.” Like Windows Notepad, it has never been developed to be a truly useful editor compared to most other GUI editors available on the market whether free (Notepad++) or purchased (Komodo, UltraEdit).
For quick and simple edits, I use vi directly on the Unix server.
Also as mentioned, if you are using a recent version of Cloverleaf, placing your root/global scripts in the Master Site is now the preferred method of making TCL scripts available to all sites on your server.
