pull them into specific folders
Not exactly: you can declare your Foundation repo as a submodule of your desktop project repo, and get those files within one specific folder.
You could then have a post-check hook in that submodule in order to copy those files elsewhere in your parent repo (where there would be ignored by a .gitignore
in that parent repo)
A submodule can be updated in a way it follows the latest commits of a given upstream branch.
See "git submodule tracking latest".