PREPARE_COMMON_DBS() - simplify main.nf by ~30%

Description of feature

Currently main.nf is dominated by PREPARE_[MODE]_DBS() subworkflows that share lots of commonality in used databases (shown after the jump).

If there was a PREPARE_COMMON_DBS() run once at the top, you can:

1. Make main.nf easier for new contributors to read
2. Highlight exactly where different modes differ in custom DB requirements
3. Massively shrink the size of the actual /subworkflows/local/prepare_[mode]_db.nf files to again just what's required from that database.

So we now have

PREPARE_COMMON_DBS(uniref30, uniref90, mgnify, pdb_mmcif, bfd, pdb_seqres, uniprot, pdb100)
PREPARE_ALPHAFOLD2_DBS(COMMON_DBS.out,  params.alphafold2_small_bfd_path, params.alphafold2_pdb70_path, ....)
PREPARE_HELIXFOLD3_DBS(COMMON_DBS.out, params.helixfold3_rfam_path, params.helixfold3_maxit_src_link ...)

More compact, less code to add new modes, but also highlights what's unique and might need custom handling.

If #203 is implemented, then we have fewer lines of code to look at downstream.
Hard support for a separate database DL subworkflow, it's time-consuming and should be separate from prediction.

main.nf DB subworkflow repetition

 PREPARE_ALPHAFOLD2_DBS (
            params.alphafold2_db,
            params.alphafold2_full_dbs,
            params.alphafold2_bfd_path,
            params.alphafold2_small_bfd_path,
            params.alphafold2_params_path,
            params.alphafold2_mgnify_path,
            params.alphafold2_pdb70_path,
            params.alphafold2_pdb_mmcif_path,
            params.alphafold2_pdb_obsolete_path,
            params.alphafold2_uniref30_path,
            params.alphafold2_uniref90_path,
            params.alphafold2_pdb_seqres_path,
            params.alphafold2_uniprot_path,
            params.alphafold2_bfd_link,
            params.alphafold2_small_bfd_link,
            params.alphafold2_params_link,
            params.alphafold2_mgnify_link,
            params.alphafold2_pdb70_link,
            params.alphafold2_pdb_mmcif_link,
            params.alphafold2_pdb_obsolete_link,
            params.alphafold2_uniref30_link,
            params.alphafold2_uniref90_link,
            params.alphafold2_pdb_seqres_link,
            params.alphafold2_uniprot_sprot_link,
            params.alphafold2_uniprot_trembl_link
        )

 PREPARE_HELIXFOLD3_DBS (
            params.helixfold3_db,
            params.helixfold3_uniclust30_link,
            params.helixfold3_ccd_preprocessed_link,
            params.helixfold3_rfam_link,
            params.helixfold3_init_models_link,
            params.helixfold3_bfd_link,
            params.helixfold3_small_bfd_link,
            params.helixfold3_uniprot_sprot_link,
            params.helixfold3_uniprot_trembl_link,
            params.helixfold3_pdb_seqres_link,
            params.helixfold3_uniref90_link,
            params.helixfold3_mgnify_link,
            params.helixfold3_pdb_mmcif_link,
            params.helixfold3_obsolete_link,
            params.helixfold3_maxit_src_link,
            params.helixfold3_uniclust30_path,
            params.helixfold3_ccd_preprocessed_path,
            params.helixfold3_rfam_path,
            params.helixfold3_init_models_path,
            params.helixfold3_bfd_path,
            params.helixfold3_small_bfd_path,
            params.helixfold3_uniprot_path,
            params.helixfold3_pdb_seqres_path,
            params.helixfold3_uniref90_path,
            params.helixfold3_mgnify_path,
            params.helixfold3_pdb_mmcif_path,
            params.helixfold3_obsolete_path,
            params.helixfold3_maxit_src_path
        )

Start in main.nf by comparing the repeated PREPARE_[MODE]DBS() calls and then inspect /subworkflows/local/prepare[mode]_db.nf for shared database handling. Refactor the common inputs into PREPARE_COMMON_DBS() and pass its output to each mode-specific subworkflow, leaving only custom database requirements in those files; done means main.nf and the mode subworkflows are substantially smaller without losing required inputs.