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comment Git Repository Source Control Process
The web page I created on gitguys.com/topics/whats-the-deal-with-the-git-index ("What's the deal with the git index") answers your question visually. It has a series of diagrams you can click through that show exactly what is changed in the working directory, index and object store (repository) when you type various git commands. (Scroll down a bit for the diagrams.)