sample.tar.gz
This applies to a case where libraries are installed (i.e. on ~/.klayout/libraries) and a file is loaded from the command line.
Apparently library reassignment does not happen: the layout is there, but the cells are not linked to the library.
Example is attached (lib_sample.gds is the layout, stdcells.gds is the library). Install the library on ~/.klayout/libraries and open the sample file with "klayout lib_sample.gds".