Make intermediate inputs reusable and modularize workflow steps

[JohGi]

• Use a prebuilt LRRome directly when lrrome is provided, without requiring the reference FASTA.
• Add an optional blast_results configuration entry to provide a merged BLAST table equivalent to blast_refProt.tsv.
• Skip LRRome or BLAST generation rules when the corresponding input is supplied.
• Split candidateLoci into:
  • candidate-locus detection from GFF and BLAST;
  • candidate-sequence extraction from the target FASTA.
• Remove the target FASTA dependency from gene prediction once CANDIDATE_SEQ_DNA has been generated.
• Refactor the workflow into stage-specific .smk files, for example:
  • lrrome.smk
  • blast.smk
  • candidate_loci.smk
  • gene_prediction.smk
  • reporting.smk