ITeamRepository repo = getRepo();
IWorkspaceHandle workspaceHandle = getWorkspace();
IVersionableHandle fileToDelete = getVersionable();
IChangeSetHandle changeSet = getChangeSet(); // Change set to check into
IWorkspaceManager wm = ScmPlatform.getWorkspaceManager(repo);
IWorkspaceConnection wc = wm.getWorkspaceConnection(workspaceHandle, monitor);
Collection ops = new ArrayList();
ops.add(wc.configurationOpFactory().delete(fileToDelete ));
IUpdateReport report = wc.commit(Collections.singletonList(changeSet ), Collections.singletonList(ops), monitor);