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Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 14: reading configurations from ~/.fonts.conf is deprecated.
As pointed out, this is a warning not an error. What it says is that the directory, ~/.fonts.conf where it found your font configuration files is deprecated. Apparently the developers of the freedesktop.org fontconfig library are in the process of moving the default location from ~/.fontconfig to ~/.config/.config/fontconfig/fonts.conf. The current fontconfig library used in 14.1RC2 (and RC1) still checks both locations for the users font configuration, but issues a warning if it finds them in ~/.fontconf. It should still work, but as they say you have been warned. It may not work in future releases of the fontconfig library. Your previous home directory, I'm guessing from a 14.0 install, obviously was using the ~/.fontconfig location. It will still work, but you will be getting this warning.
By editing the /etc/etc/fonts/conf.d/50-user,con as you did you have in effect "killed the messenger" and did not fix any bugs. If you want to get rid of the message and be in compliance with current fontconfig library defaults the do the following:
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mkdir -p $HOME/.config/fontconfig
mv $HOME/.fonts.conf $HOME/.config/fontconfig/fonts.conf
“Don’t you see that the whole aim of Newspeak is to narrow the range of thought?"