The executable, also known as ELF or SLUS on PS2 (depending on region) is the compiled binary of all of the game's code. This often includes lists the game's files, their offsets and their sizes on the disk. When the offsets do not match the true locations of the files after rebuilding an ISO, the game will read from the wrong location in memory and crash. This is why it's very important to correct the data in the executable after inserting modded files in the case of Persona 3 and Persona 4. We call this process patching.
When using the Mod Compendium for P3 and P4, the executable will automatically be patched and the new one will be saved to the Output folder along with your new CVM files. It's important to replace the original file with this one when rebuilding your modded ISO.
The PersonaPatcher was a Commandline tool created by TGE that reads a CVM and then patches the executable for compatibility. By using it, modded games can potentially be fully playable. This program has now been made obsolete by the Mod Compendium.
Usage is as follows:
PersonaPatcher.exe "%ELFNAME%" "cvm/%CVMNAME%_repacked.cvm"
The download also comes with BAT files that you can run, which will guide you through the process instead of using the program as commandline.
The following instructions come from the readme.txt:
1. Run the "Make CVM.bat" file and enter the name of the cvm you want to generate. It should generate a new CVM with the filename "cvm/x_repacked.cvm" where x is the name you specified.
2. Run the appropriate "Patch SLUS.bat" and enter the name of the game you're editing and the cvm you edited.
WARNING: Don't rename the "_repacked" file. This is the one that the SLUS is patched for.
3. The slus you placed in the /slus folder has been patched and overwritten.
4. Open the game ISO and delete the CVM(s) you're replacing and move the repacked ones inside.
5. Make sure to also replace the SLUS file.
6. Save as a new ISO.