"Does JSGME.exe allow you to just move mods in and out of the game with no problems?"
Yes, if you read the directions and use it properly - for example you install a mod that overwrites cameras.dat then manually replace cameras.dat with a different one it can blow up. JGSME is mainly for those who aren't "power users", people who are comfortable with managing and backing up safe copies of files or folders.
"What about putting multiple mods in, are they all compatible..."
No. Some mods will conflict, especially mods which overwrite the same file with different info.
"...or is there a list to show you which ones will work with which?"
Yes, if you try to install something that might conflict JGSME will pop up a warning telling you which files have already been overwritten and by which already installed mod, and gives you the option to install anyway or cancel. Not completely failsafe, if you have SH4 1.4 and install a 1.5 mod, usually it will find no conflicts but the game crashes anyway because one of the data files references 1.5 files which don't exist in a 1.4 version. For example the Weapons.upc in your 1.4 version is the original, a new 1.5 mod wants to overwrite that file, JGSME has no problem with that since the Weapons.upc file has not been overwritten by any previous mod. But the new Weapons.upc has references to U-boat weapons, and the files it's calling for don't exist in a 1.4 game. Easily fixed tho, JGSME saves a backup of the original Weapons.upc so it will replace that when you uninstall the 1.5 Das Boot mod. It actually calls it "enable" and "disable" rather than install or uninstall, but it's basically the same thing, an automated backup - copy - paste - restore gadget.
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