setup: don't modify repo in `create_reference_database()`

The `create_reference_database()` function is used to create the
reference database during initialization of a repository. The function
calls `repo_set_ref_storage_format()` to set the repositories reference
format. This is an unexpected side-effect of the function. More so
because the function is only called in two locations:

  1. During git-init(1) where the value is propagated from the `struct
     repository_format repo_fmt` value.

  2. During git-clone(1) where the value is propagated from the
     `the_repository` value.

The former is valid, however the flow already calls
`repo_set_ref_storage_format()`, so this effort is simply duplicated.
The latter sets the existing value in `the_repository` back to itself.
While this is okay for now, introduction of more fields in
`repo_set_ref_storage_format()` would cause issues, especially
dynamically allocated strings, where we would free/allocate the same
string back into `the_repostiory`.

To avoid all this confusion, clean up the function to no longer take in
and set the repo's reference storage format.

Signed-off-by: Karthik Nayak <karthik.188@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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