Deleting files outside Eclipse

I have a script that runs outside the context of Eclipse which adds,
deletes, changes and moves files from a project under Subversion
control.

However when I do a refresh + team->synchronize on the project, deleted
files are not marked as deleted but rather as incoming changes.

There doesn't appear to be a way to tell Subclipse that I really wanted
to delete the file.

I guess Subclipse somehow has to determine whether the file was deleted
locally or added to the repository. Is this facility lacking?

I have more experience using the CVS plugin in Eclipse than Subclipse
and it does not exhibit the problem.

-- 
Øyvind Harboe
http://www.zylin.com