the cleanup part in the manifest is used to get rid of files that are not necessary anymore for a specific extension, and is executed during an extension update. The "old" way to do this was to create some text files that holds the information of files to delete,
I delete log files from time to time from /Portals/_default/logs (normally before I do an upgrade of DNN, to have a smaller size of the file backup). I leave those which are only some days old.
When I uninstall an extension, I check if all the files have been deleted (you find this information normally in the manifest of the extension), esp. the assembly (in the /bin folder).
There is propably more to delete and being safe.