fix: add spectrum_id to both output dataframes for winnow predict command

[JemmaLDaniel]

Fix: Add spectrum_id column to both output files

This ensures the spectrum_id column is included in both output files generated by the winnow predict command.

Changes:

• Removed spectrum_id from the columns dropped from the metadata dataframe, so it remains in metadata.csv
• Explicitly added spectrum_id to the predictions and FDR metrics dataframe, so it's included in preds_and_fdr_metrics.csv

Impact:

Both metadata.csv and preds_and_fdr_metrics.csv now contain the spectrum_id column, enabling proper joining and identification of spectra across outputs.

[BioGeek]

LGTM.