I think you can use the .gitignore file to mention the files or path you want to ignore.
Simply, just create a .gitignore file in the root of your repo branch and list down all the files you want to ignore like
**/Packages/
**/Resources/
**/Configurations/
this will avoid all the packages, resources and configurations to be committed to the corresponding repo.
Also, let's say you have a multi-node vRO and you don't want its workflows to be synced, also add
**/Workflows/VCO@*
This should be enough. If you want to be more precise, The gitignore tutorial is here https://www.atlassian.com/git/tutorials/saving-changes/gitignore