I have modified the way 1D 'datasets' are written so that
(a) if the output prefix starts with '-' or 'stdout', then the results go to standard output (without the XML-like header);
(b) otherwise, if the -prefix option had a directory attached to the filename, then the output file will go to that directory rather than the current working directory (as was the case before).
I've also modified the 3drefit help as you suggested.
These changes are now in the source code, and will be recompiled tonight (if I remember to start the build operation before I leave).