Add option to overwrite identical files instead of renaming

Hi @harababurel!

While there is an option to rename identical files, I would also like to have an option to overwrite identical files instead of just renaming. This new option would supersede the renaming option.

Start by locating the existing option that renames identical files and trace where it is handled. Determine how an overwrite option should supersede that behavior, then verify that identical files are replaced rather than renamed when it is enabled. No file paths or tests are identified in the issue.

Written by the indexing model from the issue text.