The folder structure in GIT will be based on the elements which are **pushed** to the remote repository.
For example, if I push an entire virtual database into GIT then the folder structure will be similar to the structure which I have defined in the Virtual DataPort Administration Tool.
All the folders along with its elements like data sources, base views, etc. will have their VQL files as well as .properties/.dependencies file (based on type of element) present in GIT.
You could take a look at the [VCS Operations for GIT](https://community.denodo.com/docs/html/browse/7.0/vdp/administration/version_control_systems_integration/vcs_integration_features/vcs_operations_for_git) section under the Virtual DataPort Administration Guide for more details.
Hope this helps!