Remove `onecode` and use native RMasker hit_id to count fragments

[clemgoub]

Onecode is redundant with RM hit_id and can skip some TE if the exact nomenclature used as classification is not hard coded as regex.

Fix:

• remove onecode from repmask_vcf.sh
• update the custom RM file parser in annotate_VCF.R
• add a per-hit_id summary in annotate_VCF.R