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Date: Wed, 17 Feb 2016 18:58:18 +0100 (CET)
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From: gedau AT igor2 DOT repo DOT hu
Subject: Re: [geda-user] settings file for pcb?
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On Wed, 17 Feb 2016, DJ Delorie wrote:

>
>> Please can anyone tell me what settings/config file to create or edit,
>
> All versions of pcb should read from ~/.pcb/settings (or
> ./pcb.settings for project-specific ones).  PCB never writes to these
> files, only reads.  The contents map to command line options.
>
> GTK versions of pcb will store its preferences in ~/.pcb/preferences
> from session to session.

May it be that he is running pcb from a wrapper and the wrapper writes 
preferences for whatever reason?