well in order to include a file in your git repo you will have to add it. The fact that the file or folder exists inside your repo folder does not mean anything to git. So you need to issue a "git add" command.��
Because when you git add a folder it git adds all the files and sub folders it contain its possible to create a git ignore file that will tell git what to ignore. Again files you add inside thoses folders or new subfolders after the git add command will not be added so git ignore is not needed for those.
From what I see from working in UpdatedPharoByExample is that a gitignore is already made for all compiled files like html, pdf and anything else that pillar generated in the process of compilation so you dont need to gitignore those.��
its also possible to "git rm" this command will remove the file or folder from your git repo but it wont delete it, the file/folder will keep being inside your git repo local folder but it wont be part of your git repo and wont be tracked. ��
I can't recommend GIT DOCs enough. These guys know how to write documentation and will amazed you how simple yet powerful GIT really is.
also another thing, git add and rm commands need a git commit and git push to be uploaded and committed to you online repo. Of course you can do other modifications and actions and commit all of them with one commit and push.��