GitHub/Tower Help needed!

I’ve spent two days now trying to upload a new revision of AppleLib onto my repository, but to no avail.
The problem is I use a lot of shared code and I usually have to modify the project files so they don’t point to internal folders but to the shared folder indeed.
Everything is working nicely in my local repository.
Once I upload it, the references are not the same anymore and Xojo prompts for zillions of folders to link again.
Are there any means to upload a 1:1 copy of the local repository onto the public one?
I am about to give up and upload a Zip file of my local project only. But that’s not really what repositories are meant for.

Grateful for any hints – while Tower is nice to work with and usual projects without shared code cause no problems, I am out of ideas how to handle this issue.

Thanks a lot!

Git doesn’t change references so the best I can assume is that, when you download the project, your shared folders are in a different relative location to the new download point. You can solve this by using absolute instead of relative paths in the project manifest.

You can also try using collect project items (I think that’s the name?) to make a new project with everything together.

Thanks! @Kem: That’s what I thought I had done – everything behaves correctly when I copy the whole folder and use it elsewhere. Apparently I must have missed something and am a bit sick of fiddling around with modifying the project file. Maybe I should use
@Jasons proposal and once again make two different repositories while I still work on a singular shared project.

Do you have a vm around? Copy the whole thing there, open it, fix one or more missing files, save it and copy the xojo_project file back. That should give you a good idea of what changes are needed.