snakemake workflow broken by a rule that produces multiple files

Snakefile

shell.prefix('set -eu pipefail; ')

rule clean:
  shell: "rm -fr  in out pc *lock process.sh"

rule build_process:
  output: "process.sh"
  shell: """
    echo "#!/bin/bash

PROCESS_COUNTER=pc
(
  #getting lock
  flock 200
  #this is the "processing" step
  for i in \$@
  do  
    cat \$i | sed 's:0:A:g' > out/\$(basename \${{i/old/new}} )
  done
  #counting the number of time the processing was called
  echo \$(( \$(cat \$PROCESS_COUNTER 2> /dev/null || echo 0)+1 ))> \$PROCESS_COUNTER
) 200>lock
" > {output}
  chmod u+x {output}
  """

PAR={
  "id_list": range(1,10),
}

rule stage:
  output: "in/{id}.old"
  shell: "echo $RANDOM > {output}"

def get_all_dat(wildcards):
  out=[]
  for i in PAR["id_list"]:
    dat=rules.stage.output[0].format(id=i)
    out.append(dat)
  return out

rule stage_all:
  input: get_all_dat
  output: "in/staged.list"
  shell: "for i in {input}; do echo $i; done > {output}"

rule process:
  input: 
    list="in/staged.list",
    util="process.sh"
  output: "out/{id}.new",
  shell: "./{input.util} $(cat {input.list})"

rule plot:
  input:  "out/{id}.new"
  output: "out/{id}.plot"
  shell: "echo \"plot of $(cat {input})\" > {output}"

def get_all_plot(wildcards):
  out=[]
  for i in PAR["id_list"]:
    dat=rules.plot.output[0].format(id=i)
    out.append(dat)
  return out

rule plot_all:
  input: get_all_plot
  output: "out/plotted.list"
  shell: "for i in {input}; do echo $i; done > {output}"