In the automated rom conversion process, upernes is not doing all the job. It breaks the rom into chr and prg data and rewrites the prg code into a big assembly file called recomp.asm. It also takes care of creating a file describing the indirect jumps. The unknown indirect jump addresses must be added by the user until all of them are found (by playing the game on the snes).
The last step is made by combining the files spat by upernes with assembly files containing the emulation routines and rom banks specifications. The rom is assembled with wla-65816. This is the snes rom final product.
Today I added a shell script + makefile to convert the roms with a single shell call. They are in /source/workdir/
It will reduce development time, no need to copy everything from folder to folder and make calls everywhere.