On a case-insensitive filename platform such as Windows, 'fossil clean' may prompt to delete files that aren't reported by running 'fossil extras'. I would expect 'clean' only to prompt to delete the same files listed by 'extras'.

In checkin.c, the function clean_cmd() appears to generate a file list using:
  db_multi_exec("CREATE TEMP TABLE sfile(x TEXT PRIMARY KEY)");

While the function extra_cmd() uses:
db_multi_exec("CREATE TEMP TABLE sfile(x TEXT PRIMARY KEY %s)",
                filename_collation());

So I think the fix is to use filename_collation() in clean_cmd() too.

In my repository, the two files that 'clean' prompts for deletion were originally added under a "docs" sub-folder that has since become "Docs".

Thanks
Mark.

Unlike 'fossil extras', 'fossil clean' doesn't consider case-sensitivity