[samhornstein]

Add an import and Nextflow staging example for the MEGARes 3.0.0 resistance FASTA and matching annotations used by FloRes. The helper verifies pinned checksums and matching records, records provenance, resolves a Workbench bucket resource, uploads with generation preconditions, and produces a params file for CLI or Workflows UI runs.

The standalone workflow stages both reference files as task inputs and verifies their hashes and counts. The guide maps them to FloRes's amr and annotation parameters; the full database is not committed. Partial upload retries reuse the same local receipt; a fresh fetch with a different timestamp needs a distinct prefix to preserve both receipts.

Validation

• Eight offline helper tests passed, including checksum rejection and mocked upload failures/retries.
• The standalone workflow passed against the baseline config with the synthetic fixture (2 sequences, 16 bases, 2 annotations).
• The full FloRes MEGARes pair passed locally: 8,733 sequences, 9,014,529 bases, 8,733 annotation rows, and matching pinned hashes.
• Documentation links and whitespace checks passed.
• Publisher download could not be exercised because its domain is blocked here. Real GCS upload and Workbench/Batch execution remain pending; test steps are in the guide.

Jira: BENCH-9861