When converting directories offer the user a list of types so that we only convert those files that the user wants converted.

When the user pick files in Nautilus he or she can see which types they are (usually anyway) but if a directory is picked it could be full of files of all different types when the user only wants to convert from, say, flac to ogg.

When we detect that user has included directories add all the possible input formats as check boxes to a dialog. The user must specify at least one. Make the default values part of the config file.