Modify combined_compounds output format: move in silico annotations from row names to dedicated columns

[KevinBillet]

In the current examples, the combined_compounds output uses row names to store in silico annotation information. To improve data handling and facilitate further processing, these annotations should be moved into explicit columns within the resulting data frame.

Specifically:

• Remove annotation information from the row names.
• Include all relevant annotation details as dedicated columns in the combined_compounds table.
• Ensure that the output remains compatible with downstream analysis and visualization steps.

This change will improve clarity, make data manipulation easier, and align with tidy data principles.