Improve Return List Structure in ExtractCore

[jibarozzo]

Description:
The ExtractCore function currently returns an unnamed list, which can be confusing for end users to navigate. This issue proposes improving the return list by using named elements with informative and consistent naming conventions.

---

Current Implementation

return_list <- list(core_otus, BC_ranked, otu_ranked, occ_abun, otu, map, taxon)
return(return_list)

Proposed Implementation

return_list <- list(
  core_otus = core_otus,               # Core OTUs identified
  bray_curtis_ranked = BC_ranked,      # Bray-Curtis dissimilarity rankings
  otu_rankings = otu_ranked,           # OTU occupancy/abundance rankings
  occupancy_abundance = occ_abun,      # OTU occupancy and abundance data
  otu_table = otu,                     # OTU table (samples x OTUs)
  sample_metadata = map,               # Sample metadata
  taxonomy_table = taxon               # Taxonomy table
)
return(return_list)

Before

results <- ExtractCore(...)
core_otus <- results[[1]]  # Unclear and error-prone

After

results <- ExtractCore(...)
core_otus <- results$core_otus  # Clear and self-documenting

@B-Kristy @Gian77