Replace the `dir_filter` with a `path_filter` in `Directory`

`dir_filter` only filters directories. `swh-scanner` needs to
accurately filter out ignored files before making expensive requests
to the web API. We introduce a more general `path_filter` that allows
us to differentiate between files and folders.

`dir_filter` is now deprecated and will be removed once the remaining
users in other packages are migrated over to the new API.

`accept_all_directories` is also deprecated, because it only implies
accepting *directories* even though its behavior also accepts
non-directory entries when used with `path_filter`.