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Because renaming files and moving them between directories is somewhat inconvenient, the first thing you do when you start a new project should be to think through your file organization. It is not impossible to rename or move files, but it does increase the potential for confusion and CVS does have some quirks particularly in the area of renaming directories. See section 7.4 Moving and renaming files.
What to do next depends on the situation at hand.
3.1 Setting up the files Getting the files into the repository 3.2 Defining the module How to make a module of the files