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Also, can PHP script under one vhost read/write files under another vhost? I have several domains with ads, and like to run a tracking script common to them all.
Use SCP instead. There are many graphical front-ends for scp. Your username and password are encrypted along with the rest of the traffic.
the format from teh command line (*NIX box) is simple:
scp locafilename.tgz remotehost:/path/to/remote/location
You can also set up authorized keys to use, so you don't even have to enter in your username and password, it's all based off of your public key (SSH key). Although not so secure as well, if you trust the box you're on, it can be a time saver.
However, you can safely use most modern FTP clients to transfer files using the SFTP capabilities of the SSH2 protocol. Off the top of my head, I know for sure that Transmit (Mac) and CuteFTP (Windows) support it, as does gFTP (Linux/Unix). Depending on the program, it may be called "SFTP", "Secure FTP", or "SSH2". These are all the same thing, and can be used with the OpenSSH server that is installed by default anymore on any *nix system worthy of the name, including RHEL 3. If you don't need anonymous FTP, you can just uninstall your FTP server, and I recommend you do just that.
Better yet, for your purposes, run a local X server. Then you can just ssh to the server and run your editor from the command line, but get a pretty local-looking editor window that you can point and click at to your hart's content, without ever downloading and uploading the file. I do this all the time, and it's my favorite way to deal with small changes to remote files.
Unix desktops run X for their graphical interfaces anyway. (Unless they are Macs.) On Windows it's a bit harder, and I haven't used Windows in too long to tell you how. On a Mac, either install Fink (fink.sourceforge.net, I think) or if you have OS 10.3, just install the X server from the 3rd disk.
As for PHP scripts working on files in different vhosts, sure thing. The PHP script has access to the machine's file system. There might be file ownership and permission issues to work out, but it can certainly be done.