Add direct RGP to gene families mapping output

[JeanMainguy]

Summary

This PR adds a new output option --regions_families to the write_pangenome command that generates a simple TSV file mapping Regions of Genomic Plasticity (RGPs) directly to their gene family content.

Motivation

Previously, analyzing the gene family composition of RGPs required a multi-step workflow:

1. Export gene pangneome annotation with RGP info using ppanggolin write_genomes --table
2. Map genes within an RGP to their families using the gene_families.tsv file
3. Join these files to obtain RGP-to-family mappings

This indirect approach was quite complicated and was necessary to process many files from the write_genomes command.

Changes

• Added --regions_families flag to ppanggolin write_pangenome command
• Generates rgp_families.tsv with two columns:
  • rgp_id: RGP identifier (matching the 'region' column in regions_of_genomic_plasticity.tsv)
  • family_id: Gene family identifier present in the RGP
• Updated documentation in docs/user/RGP/rgpOutputs.md with usage examples and column descriptions

Usage

ppanggolin write_pangenome -p pangenome.h5 --regions_families -o rgp_outputs