The Calling sequence is

Make a mask
phase_slope -> Calculate the phase gradient in range and azimuth and threshold on gradient value
phase_mask -> Calculate a mask using the phase standard deviation, this calculation requires the phase slope

Compute residues
residue -> Compute the residues and create a flag file
trees -> Connect the residues and modify a flag file
corr_flag -> Modify the residues in the flag file using a correlation threshold, although this programs name implies 
             that the interferometric correlation is used, currently ROI_PAC uses the mask generated by phase_mask.
grass -> Unwrap the interferogram

The flag file has a zero value for regions with no residues, and a non-zero value for regions with residues.