Edited the g5k:generate rule of the Rakefile. It now passes clustername/nodes/*.yaml to the generator instead of clustername_generated.yaml.
Also modified lookup() calls in the .rb file of each cluster using:
 for i in $(find . -iname "*.rb"); do name=$(basename $i .rb); sed -i "s/lookup('"$name"_generated', /lookup(node_uid, /g" $i; done

    - Split <cluster_name>_generated.yaml files to cluster/<cluster_name>/nodes/<cluster-name>-[uid].yaml
    - Moved <cluster_name>.rb and <cluster_name>_manual.yaml to cluster/<cluster_name>/
    - Created empty <cluster_name>_manual.yaml for Lyon (otherwise, rake script does not work with SITE=lyon as those input files do not exist)

    --

    For the record:

    From generators/input/sites/:

    cluster_list=$(ls ./*/clusters/*generated.yaml)
    for cluster_file in $cluster_list
    do
        (
    	cd $(dirname $cluster_file)

    	cluster_name=$(echo $(basename $cluster_file) | cut -d '_' -f1)
    	echo $cluster_name

    	last_node_number=$(egrep $cluster_name- *_generated.yaml | cut -d "-" -f2 | cut -d ":" -f1 | sort -n | tail -n1)
    	#echo $last_node_number

    	mkdir -p $cluster_name/nodes/ 2> /dev/null
    	for i in $(seq 1 $last_node_number)
    	do
    	    (
    		echo "---"
    		echo "$cluster_name-$i:"
    		sed -n "/^$cluster_name-$i:$/,/^$cluster_name-.*:$/p" $cluster_name"_generated.yaml" | sed "/^$cluster_name-.*:$/d"
    	    ) > $cluster_name/nodes/$cluster_name-$i.yaml
    	done

        )
    done

    find . -iname "*_generated.yaml" -exec git rm -f {} \;
    git add */clusters/*
    for i in $(ls -d */clusters/*.rb); do (cd $(dirname $i); git mv $(basename $i) $(basename $i .rb)_*yaml $(basename $i .rb)); done

    (+ manually fixed lyon)