I confused the concept of Git submodules.
I created separate repositories intended to be submodules of another project, then in the main project repository I added empty folders to where these files should be added.
example:
MyProject/
./lib
./headers
./source
those folders are empty because the contents will be coming from the separate repos as submodules but the thing is that they are named differently.
the contents of lib/ will be coming from lib_trunk submodule and source is called source_trunk
is there a way to tweak the submodules feature in git to instead clone the repo as named it will just add the files contained in the repository?