The Dockerfiles.git directory is the place where Dockerfiles that are used to create containers that use the upstream git code live. These Dockerfiles are meant to be used to build an atomicapp base container for a number of different base operating systems.
For example, if you want to build an Atomic App container for Debian that uses the upstream git code then you would run the following command from the root of the git repo:
docker build -t debian-atomicapp-git -f ./Dockerfiles.git/Dockerfile.debian .
If you want to do the same thing for Fedora you would:
docker build -t fedora-atomicapp-git -f ./Dockerfiles.git/Dockerfile.fedora .