"evalfold.hh" is for RNAeval-like behaviors for Bellman's GAP programs: first input is the RNA sequence, second input must be a structure in Vienna-Dot-Bracket format. The idea is to "abuse" the base-pair filter such that it only allows for the right positions to pair. In addition, the terminal parsers BASE or REGION must enforce to be unpaired, otherwise we get a set of structure with all or just some of the given basepairs.
Furthermore, the generated out_main.cc must be modified to pass the second input to the global Pairs object and remove it before the real algorithm starts. Do this via the Misc/addRNAoptions.pl script!