refs.c: rename ref_array -> ref_dir

This purely textual change is in preparation for storing references
hierarchically, when the old ref_array structure will represent one
"directory" of references.  Rename functions that deal with this
structure analogously, and also rename the structure's "refs" member
to "entries".

Signed-off-by: Michael Haggerty <mhagger@alum.mit.edu>
Signed-off-by: Junio C Hamano <gitster@pobox.com>