If I understand correctly...JSGME temporarily swaps files within a designated directory. For example: If a particular file, say abc.dll, needs to be modified and it is in the file directory, say DCS\somefolder\someotherfolder\abc.dll, and there is a JSGME Mod called abcmod, the modified file would be in the JSGME mods folder and would be in a folder structure that looks something like this abcmod\DCS\somefolder\someotherfolder\abc.dll. So the directory structure for the original game file is just mimicked inside the folder with the mod name ie; abcmod folder.
So that particular iteration of JSGME would be set up to look in the DCS folders for any matching files in the appropriate folder directory structure when you activate a mod. It temporarily replaces the matching game file with the modified file and swaps them back when you deactivate the mod.
That is why mod activation order is sometimes important. Sometimes after one mod is activated a second mod may replace files in the same directory or even the same file as the first mod did, so JSGME generates a warning that you may be tinkering with a file that has already been swapped and could be potentially removing or changing the first mod (sort of modifying a mod...potentially dangerous.)
Let me know if this makes sense or if I am incorrect. Also where JSGME is installed and at which File directory it is initially pointing affects the particulars of the file directory structure. My example above is completely fabricated and a generalized representation. If you look at one of your existing JSGME Mods, you can chase through the folders and see what files are being replaced when it is activated by comparing it to the game file directories for whatever game that iteration of JSGME is being used.
