dk dep is too slow

[fblanqui]

dk dep takes more than 11 minutes to compute the dependencies of the 111 dk files generated by isabelle_dedukti for the HOL standard library. This is more than the time needed by dk check (10 minutes) to check those files in topological order (which is generated by isabelle_dedukti in less than 1s). To reproduce the problem, follow the instructions on https://github.com/Deducteam/isabelle_dedukti.