Check out Aemulus Package Manager for Automated Bin Merging!
I'm making this tutorial since people keep asking about my mods not showing up due to being overwritten.
Before Starting You'll NeedAmicitia by TGE. Simply download the latest release and unzip it and its ready for use. This is the only tool needed for merging the files.
ProcessI'll be merging my P5 Overhaul mod and MudKip's Skill and Persona Pack for this tutorial.
1. You need to check if multiple mods are modifying the same bin files. I could see that both mods have init_free.bin and init.bin in the data00004 folder.
Common Files To Be Merged:
2. Open up the bin file in Amicitia. You can do this by dragging the file onto the interface or clicking File->Open and open the file from there.
3. Now come's the trickiest part. You'll need to find out which parts of the bin file each mod changes. You can either ask the creator of the mod to specify what they edited or find out yourself. Finding out yourself is easier for sprites which you can preview in Amicitia. In this example case, we'll first look through my Mudkip's init_free.bin. It's not evident what exactly is modified since no images that can be previewed are changed. Instead I found from his comments that he edited MSG.TBL, SKILL.TBL, and PERSONA.TBL. As for the P5 overhaul mod's init_free.bin, we could see that a lot of the Textures in init/camp.arc/c_main01x02.spr are modified.
The init.bin files have no sprites to preview at all so I'll just tell you that my P5 Overhaul only modifies system/font/font0.fnt and I'm not 100% what the skill mod modifies.
4. Now we need to export the modified files from one of the bin to a temporary location such as the Desktop. Since the skill mod only modifies 3 files compared to the many more textures of the P5 overhaul mod, I decided to export the previously mentioned TBL files from the skill mod's init_free.bin. To do this right click the modified file and click Export. We have to rename it since '/' is an illegal character to save a file as. I'll just remove the 'battle/' so I'll remember which files I need to replace. Then just click save.
I'll do the same for the P5 overhaul's init.bin's system/font/font0.fnt and save it as font0.fnt.
5. Next we'll replace the other bin's files with our recently exported files. To do this, we'll open the P5 overhaul mod's init_free.bin in Amicitia. Right click on the files you previously exported from the other init_free.bin and click Replace. Find the file you saved in a temporary location and open it to finish replacing it. We'll do the same when replacing the skill mod's init.bin's system/font/font0.fnt
6. All you have to do now is click File->Save As to create a new bin file with both mods combined. Use this new bin file in your mods folder and you should see both mods are combined.
As you can see the P5 UI and the new skills are both in game.
Note that you cannot combine the mods if they modify the same part of the bin file. One must overwrite the other. Let me know if any part of the tutorial is unclear.