If you're sure that's what you need to do, you can add rules in the source under nuspackage/packaging/ContentRules.java, then make a new jar file. Be sure to specify the correct fstflags.
It's more likely that you don't have your input folder set up properly (code,content,meta), or you didn't specify a -in folder and empty -out folder on your command line. What kind of a package are you making that includes a fw.img, and which of the three directories do you have it under?
Well, I struggled a bit with -in and -out folder, since even though I specfied those, the program always was telling me it didn't find them and created an "output" folder, which I started to use after some failed attempt. I will look into that tomorrow, I probably fucked up something stupid.^^'
And I knew that someone would ask because of "fw.img". xD WiiVC games include those in the code folder. I try to repackage Super Mario Galaxy 2. FTPiiU doesnt let me replace the nfs files, those have some sort of special permissions, even Fix doesnt know exactly whats going on there. So repacking is the only way to test some modifications on the eggs header... I'm pretty sure this wont work either, but you neher know...