ref-filter: introduce struct used_atom

ref-filter: introduce struct used_atom

Introduce the 'used_atom' structure to replace the existing
implementation of 'used_atom' (which is a list of atoms). This helps
us parse atoms beforehand and store required details into the
'used_atom' for future usage.

Helped-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Karthik Nayak <Karthik.188@gmail.com>
Reviewed-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>