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.