Actually, I was thinking about including some instructions on how to use the command line, but since that wouldn't be related to this program specifically, I decided not to. I would also have to write the same instructions for every command line utility and that seems a bit unnecessary, at least to me.

I guess you probably have figured out how to do it by now but since you asked, I can give you some hints anyway.

If only one argument needs to be passed and that argument is a file, then the easiest thing to do is drag the file and drop it on the program's icon.

If more than one argument needs to be passed I would recommend typing them manually from the command line.
One thing you can do, that I find quite convenient if you want to do the same thing many times, is make a .bat file. In your case you would write something like:
in a text file and give it the extension .bat and put it in the same directory as the program and the files and then just double-click it to run.
The 'PAUSE' is there so you can see the output of the program before the window closes.

Maybe I should also point out that if your need for remapping is because of a tileset rearrangement then you should use the other utility 'J2T Rearranger' to generate the 'swapfile' while you rearrange.

Well, I hope you find this helpful, and I'm glad you use my program