How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1.

That would be possible, with a few contortions, but why do you want this? Do you want to switch between phenix.refine and refmac? refmac has an option to specify the flag value for the free set. phenix.refine detects the free set automatically. CNS usually uses 1 for the free set, but it is a parameter you can change. Ralf