config_file: move include depth into config entry
In order to reject writes to included configuration entries, we need to keep track of whether an entry was included via another configuration file or not. This information is being stored in the `cvar` structure, which is a rather weird location, as it is only used to create a list structure of config entries. Move the include depth into the structure `git_config_entry` instead. While this fixes the layering issue, it enables users of libgit2 to access the depth, too.
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