The instructions with the program just tell you to install it into the SH4 folder:
C:\Program Files\Ubisoft\Silent Hunter Wolves of the Pacific\JSGME.exe
I also don't have a Start Menu shortcut or anything in my Add/Remove Programs. I assume all the setup does is copy the JSGME.exe file and create the MODS and !BACKUP folders. That's it. It may be written in .Net and not need any additional files installed except just the .exe.
It would be nice if they included an uninstall option like most users would expect. But I think you can just delete the .exe and MODS folder and be ok.
It appears that the info about what mods are installed is saved in a file called JSGME.ini which is in the MODS folder. I have not tried this, but if you delete (or just move it to be safe) this file, I'm guessing your Mods will not appear to be installed anymore. If that doesn't work, try editing the file and removing the list of installed mods.
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