It is possible to “officially” ignore files by extension, or ignore files & directories by name, but the option to do so is found under the “Server Options” of Surround which might be locked down by the administrator, and even if it isn’t, the changes would apply to all users which might not be desired.
However, I did stumble across one possible solution, (functional though inelegant), for just a single single client or user to set up a personal set of ignored files/folders.
All you have to do is set the files or folders as “hidden” in Windows Explorer. Then, Surround just ignores them. It’s sufficient to hide just a parent folder – the hidden attribute for any subfiles or subfolders won’t matter, Surround will ignore them all as long as the parent folder is hidden. Hidden files won’t show up anywhere in Surround, either when looking at “Working Directory Differences” or in the “Add Files” dialog.
While this isn’t as flexible as defining a set of rules (say, all files of a certain extension) it’s better than nothing.