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The layout of the packages in a repository is not fixed. You can place a single package into the root of the repo (e.g. https://github.com/ros/genmsg) or you can put packages under a hierarchy of folders (e.g. https://github.com/ros/ros_comm).

The folder name / repository does not have to be identical to the containing package name but usually that is a good idea since that is what a user would usually expect.