Remove row names from study_case_extended and ensure annotations are stored in explicit columns

In the current implementation, the study_case_extended result table includes row names that do not consistently correspond to the information present in the columns. This can cause confusion and hinder data handling.

Requested changes:

• Remove all row names from the study_case_extended data frame.
• Ensure that all relevant annotation and identification information is fully captured within dedicated columns.
• Verify that row names do not duplicate or conflict with existing column data, and eliminate any ambiguous or redundant identifiers.

These improvements will enhance data clarity, consistency, and facilitate downstream analyses.