In scripts/os-eap-s2i/added/s2i/assemble

IFS=',' read -a install_dir_entries <<< $CUSTOM_INSTALL_DIRECTORIES
  for install_dir_entry in $install_dir_entries; do

reads only the first item of the comma-separated CUSTOM_INSTALL_DIRECTORIES... (it is an array, so something like

for install_dir_entry in "${install_dir_entries[@]}"; do

should be used instead...