Split cleanData and add Parquet exports

[AbhirupaGhosh]

Rename the original cleanData to cleanMetaData and add roxygen skeleton. Introduce a writeCompressedParquet helper and export cleaned metadata, AMR phenotype, genome data and original metadata to compressed Parquet files, then create a separate DuckDB (parquet-backed) with views for metadata, amr_phenotype, genome_data and original_metadata. Reintroduce a new cleanData function focused on feature matrices (genes/proteins/domains/etc.) that writes feature tables to Parquet and creates corresponding views; remove duplicated metadata parquet exports from the feature-matrix flow. Minor whitespace and path-handling adjustments to normalize paths and ensure output directories exist.

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