It might help to think of your SVN experience.  In SVN when you checkout 
a branch, you download a *copy* of the files in that branch in the repo. 
When you commit, you upload your modified files to the branch in the 
repository.

In Git,  although you have your version of repository in a database on 
your computer, the situation is similar. In Git, when you checkout a 
branch Git loads the files in that branch from the repo to the working 
directory, where they show in your file system and you can open them and 
modify them.  When you git commit them, the changes are written to the 
repo.

In both Git & SVN, you generally make changes to your repository using 
your vcs commands, and you make changes to the checked-out copy using 
your editor.  In both cases, branches exist *in* the repository, and the 
files that you are working on have come *from* the repository.  The 
difference is that in Git the repo you are working from is your personal 
version which is stored on your computer.
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