The runCA docs have a handful of sample spec files. Are these complete? Easy to find?
Add, in the source distribution, a larger set of spec files (bacteria, dros, human, metagenomic). Include comments in them.
Add a mostly-complete specfile that describes all the major switches and tunables. This specfile does not need to, and probably should not, make sense if it is used to run the assembler. Its purpose is to give the user something to cut-n-paste from.