I don't know the SCM server APIs.

Some considerations about the SCM Server API are here: https://rsjazz.wordpress.com/2016/02/03/setting-access-control-permissions-for-scm-versionables/

The client API looks as follows:

    private void setFlow(IWorkspaceConnection source,
            IWorkspaceConnection dest, Collection<icomponenthandle> components,
            IProgressMonitor monitor) throws TeamRepositoryException {
        // Get the current flow table
        IFlowTable cflowTable = source.getFlowTable().getWorkingCopy();
        // Set the accept and deliver flow to the target
        cflowTable.addAcceptFlow(dest.getResolvedWorkspace(), dest
                .teamRepository().getId(), dest.teamRepository()
                .getRepositoryURI(), components / Collections.EMPTY_LIST /,
                "Accept Flow");
        cflowTable.addDeliverFlow(dest.getResolvedWorkspace(), dest
                .teamRepository().getId(), dest.teamRepository()
                .getRepositoryURI(), components / Collections.EMPTY_LIST /,
                "Deliver Flow");
        // Limit the scope for accept and delivery to the components that are
        // needed
        cflowTable.setComponentScopes(dest.getResolvedWorkspace(), components);
        // We want incoming and outgoing default and current flow
        // Set the incoming flow for current and default
        IFlowEntry acceptEntry = cflowTable.getAcceptFlow(dest
                .getResolvedWorkspace());
        cflowTable.setCurrent(acceptEntry);
        cflowTable.setDefault(acceptEntry);
        // Set the incoming flow for current and default
        IFlowEntry deliverEntry = cflowTable.getDeliverFlow(dest
                .getResolvedWorkspace());
        cflowTable.setCurrent(deliverEntry);
        cflowTable.setDefault(deliverEntry);

    // Set the modified flow table
    source.setFlowTable(cflowTable, monitor);
}

</icomponenthandle>