Pathnames can be either full or relative. Just make sure that for relative pathnames you are in the correct directory as no attempt is made to check that the file can be found.
At the end of using pregap, numerous files will have been created. If SCF files are being produced, or were used as the input file type, a list of these will be found in "fofn".scf (where "fofn" is the file of input filenames specified). If Experiment files are being created (but not if they were the input files) then the list of these files is in "fofn".exp.
In addition to these "fofn".passed and "fofn".failed contain the list of successful and failed experiment files. If repeat segments were not searched for then "fofn".passed should be used as the input to the gap4 (or xgap) "Assemble" option. Otherwise two more files, "fofn".repe_passed and "fofn".repe_failed will have been created: assemble the "fofn".repe_passed file followed by "fofn".repe_failed.
Finally, "fofn".entry contains a list of the EN line types used in the experiment files created. This line type specifies the reading name used within gap once this Experiment file is assembled. Normally the EN line is the same as the filename, but in cases where this conflicts with the corresponding trace filename pregap appends ".exp" to the filename, keeping the original filename as the 'entry name' (EN line). Note that the "fofn".entry file is generated whilst creating the experiment files. Hence there maybe more lines in this file than the final "fofn".passed file if Readings have failed during later processing stages.