Martek: Please read my long post where I describe the issue:
The person in your link explained why it was moved, why the file is out of place. It's not needed for GOG's version to work fully.
If your installing a mod its your responsibility to edit the install to work with it. Your changing and modifying the base delivered game from GOG. I'm with the guy in your previous post on this, GOG should not be expected to keep a release "mod ready" if it could potentially hurt the over all game as its sold in its default state.
Always best to play it cautions and hand install all prerequisites for mods to ensure full compatibility. That said, moving that one file
squirrel.osm from docs to base should be a stickied solution to get modern mods to work.