refactor create-directory-structure, and create 'clone_repo' function

We'll need "cloning a repo again" for 'available' command, so I'll try to put that in a dedicated function (clone_repo).

Once I have done that, the 'create_dir_structure' function is basically empty. So I have moved that into the prepare function - the only place from where create_dir_structure was ever called. (This should better have gone into a separate MR I think now, sorry.)

The diff looks a bit confusing because git mixes up the create_dir_structure and the "cloning a repo" function.

Minor adjustments to debug information.

The work for the 'available' command will be based on these changes.