When upgrading a package, we compare the new file list to the file list in the local db and only look at the difference when looking for conflicts. This can miss issues and cause pacman to abort part way through.

e.g.
filesystem has file "/var/run" and a user replaces it with a directory. Next filesystem update, pacman refuses to extract the /var/run file over a directory and bails.


We can address this by checking the file types of the intersection of the file lists, but that may be slow... But perhaps the extraction phase might speed up in compensation due to all files being previously accessed?