Ensure concatenated reference FASTA temp file has .fasta suffix

[wwood]

Summary

• add a .fasta suffix when generating concatenated reference FASTA files so mappers that require the extension accept the temp file
• add a unit test to guard the concatenated FASTA extension and content
• clean up Clippy warnings in existing code that were triggered by the new lint run

Testing

• cargo clippy -- -D warnings
• cargo test mapping_index_maintenance::tests::concatenated_fasta_file_has_required_extension

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Codex Task