(Outdated): TGE’s solution to a formidable obstacle that PS2 game modders must face: the executable. Normally, replacing files would lead to the game not finding data where it expects it, but the aptly named patcher reads your new CVM files and generates a new executable that adheres to the offsets of your new files.
The download also features a guide and some batch files courtesy of Shrinefox for those more intimidated by command prompts. Included as well is the CVMtool that splits CVM files into ISOs and header files for further editing.
Note that this program is not yet 100% compatible with Persona 3, but you may use a custom version of PersonaPatcher Golden that supports 3 by using a combination of new and old versions of the program: