SD copies folder inside script app to location of link to that folder

This one took me years to figure out, but I should have seen it a long time ago.

I have some scripts that use the Wineskin software to run Windows applications. My scripts contain a Wineskin app that in turn contains multiple levels of folders leading to a Windows program folder that I modify often. For convenience, I have a symbolic link in the Contents folder of my applet that links to that folder deep inside. That link looks like this when you get a directory with ls -l command:

vDosProgramFolder -> ../Contents/Resources/ Files/vDos

When I edit this application in SD, and save it, SD makes a copy of the linked folder and places the copy in the same high-level folder with the symbolic link. This simply wastes space, because the newly copied folder isn’t used for anything.

I suppose the solution to this issue is “Don’t put that link there”, but is it possible that SD should not be copying the folder when it finds the link? Is this what it is designed to do? If so, is there a workaround that would let me access that folder deep inside the app in a simple way?

I may be the first person who encountered this issue (if it is an issue) so I don’t expect anyone to spend much time on it.