I’ve search high and low for a good solution to this that allows me to keep my project folders on my Desktop but haven’t found anything. Apparently the Desktop, Documents, and Downloads files are just more strict now. I’m thinking macOS just thinks any change to a file that tries to access other files in these three folders is potentially nefarious and they try to play gatekeeper. It was obviously done as part of their security updates in moving towards tighter security but this is just such an unnecessary hiccup for developers.
Anyway, the only two solutions I’ve seen that work (I’m using Xcode, personally) is to move folders outside of the three folders I named earlier, or just run directly through the Terminal app rather than through an IDE. This obviously isn’t perfect, but it works. I don’t like not having my important projects on my Desktop anymore but until I find a better solution I guess that’s what I’ll do.