Came here to say the same thing. The git book is an afternoon's reading. It's well worth the time - even if you think you know git.
People complain about the UX of the cli tool (perhaps rightly) but it's honestly little different from the rest of the unix cli experience: ad hoc, arbitrary, inconsistent.
What's important is a solid mental model and the vocabulary of primitive and compound operations built with it. How you spell it in the cli is just a thing you learn as you go.
What are the permissions on the directory? What is command are you running to edit the file? What command are you running to delete it? (Have you got selinux turned on? What filesystem is this directory on?)