I've been using rtorrent for a while with a single directory. Now I figured out it was possible to use different directories and even to move completed downloads elsewhere, so according to the rtorrent wiki I edited my .rtorrent.rc as follow :

# Download directory
directory = /Medias/torrents/

# Watching directories
schedule = watch_directory_1,5,60,"load_start=/path/to/dl/dir1/*.torrent,d.set_custom1=/path/to/done/dir1"
schedule = watch_directory_2,5,60,"load_start=/path/to/dl/dir2/*.torrent,d.set_custom1=/path/to/done/dir2"

# On completion, move the torrent to the directory from custom1.
system.method.set_key = event.download.finished,move_complete,"d.set_directory=$d.get_custom1= ;execute=mv,-u,$d.get_base_path=,$d.get_custom1="

It seems to work for new torrents. However I have a bunch of completed files I have already downloaded before to split directories, and for them it does not work : if I delete their file in the session directory, rtorrent will check the hash but won't move them, and if I move them by myself rtorrent won't see them and will try to redownload them.

So how can I tell rtorrent either to move them or that they are in another directory ?

Thanks.