Fix Docker errors, add R.utils import, manifest diagnostics

[eboyer221]

Summary

• Fix .mergePanaroo() discarding its system2() result entirely, so a failed panaroo-merge run inside Docker previously failed silently. Now checks exit status and surfaces Docker's output, matching the pattern already used in .processPanaroo().
• Add the same exit-status check alongside the existing missing-output-file checks in .runCDHIT(), .runHmmerJob(), and both hmmpress/hmmsearch call sites in .defenseHMMER(), so Docker failures are caught by exit code, not just inferred from a missing file.
• Add R.utils to DESCRIPTION Imports, it's used by .prepareHmmerDatabases() to gunzip the Pfam HMM download but was never declared as a dependency.
• runDataProcessing()'s clean_metadata_and_export manifest stage now records the 5 specific reference TSVs cleanMetaData() reads (clean_drug.tsv, drug_class.tsv, drug_abbr.tsv, class_abbr.tsv, cleaned_bvbrc_countries.tsv) as inputs, instead of just the ref_file_path directory.

Closes #59, #58. Addresses the remaining part of #48 (the Parquet-output itemization was already in place on main).

Test plan

• devtools::test() — 46 passed, 0 failed, 0 skipped
• roxygen2::roxygenise() — no doc changes needed (internal logic only)
  EOF
  )"