It’s nice you have reacted so fast. The proposed solution is the step in right direction, however, I would propose the following changes:
1. Don’t duplicate the input values. The application which generates the query knows what it is asking for, so the input values in the output file will be discarded. Only additional hassle.
2. Instead of the output file use the standard output. If the user wants to have a file he will use the stream redirection fuzzylite -i engine.fll -d inputs.fld > output.fld. It is how the MATLAB stuff works. However, I don’t know if it works also under Windows, but if it doesn’t then you can have the -o option and the standard output, if no file was defined. Obviously, to the standard output you should not send the header with the description.
The decision is yours, I can use any setup.