Local changes to texmf.cnf?

[Gregory Heytings]

>
> Try the following in a shell:
>
> kpsewhich -a texmf.cnf
>
> to see the order.  HTH.
>

Thanks a lot, it does help!  This was the missing piece, I did know about 
kpsewhich but did not know that it was used for config files, too.  FTR, 
on Debian local modifications to texmf.cnf are in /etc/texmf/texmf.d/, and 
update-texmf generates a /etc/texmf/web2c/texmf.cnf file.