Expanded the CI pipeline to include more subcommands and file comparisons.

• run build_panproteome
• run export_panproteome (local)
• compare panproteome exports
• run add_annotations
• compare db/proteins/
• run add_phenotypes
• compare db/phenotype_overview.txt
• run group
• run grouping_overview (local)
• compare db/pantools_homology_groups.txt
• compare db/group/grouping_overview.txt
• run add_pav
• run add_variants
• run variation_overview (local)
• compare db/variation/variation_overview.txt
• run add_functions
• run functional_classification (local)
• compare db/function/functional_classification/functional_classification_overview.txt
• compare db/function/functional_classification/core_functions.txt
• compare db/function/functional_classification/accessory_functions.txt
• compare db/function/functional_classification/unique_functions.txt
• run function_overview (local)
• compare db/function/go_overview.csv
• compare db/function/interpro_overview.csv
• compare db/function/pfam_overview.csv
• compare db/function/tigrfam_overview.csv
• run go_enrichment
• compare db/function/go_enrichment/go_enrichment.csv
• compare db/function/go_enrichment/go_enrichment_overview_per_go.txt
• run gene_classification (local)
• compare db/gene_classification/gene_classification_overview.txt
• compare db/gene_classification/classified_groups.csv
• run kmer_classification (local)
• compare db/kmer_classification/kmer_classification_overview.csv
• run pangenome_structure
• compare db/pangenome_size/gene/core_accessory_unique_size.csv
• compare db/pangenome_size/gene/core_dispensable_size.csv
• compare db/pangenome_size/gene/core_dispensable_total_size.csv
• compare db/pangenome_size/gene/pangenome_size.txt
• run pangenome_structure --kmer
• compare db/pangenome_size/kmer/core_accessory_size.csv
• compare db/pangenome_size/kmer/core_accessory_unique_size.csv
• compare db/pangenome_size/kmer/pangenome_size_kmer.txt
• run msa
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/genome_order.info
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/sequences.info
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/skipped_genomes.info
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/trimmed.info
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/var.structure.tsv
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/var.fasta
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/output/var.fasta
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/input/prot.fasta
• compare db/alignments/msa_per_group_var/grouping_v1/<group>/output/prot.fasta
• run ani
• compare db/ANI/MASH/ANI_distance_matrix.csv
• run core_phylogeny
• compare db/core_snp_tree/sites_per_group.csv