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I can change the hinting and sub-pixel settings from /etc/fonts/conf.d or gnome-tweak-tool. What's the difference of those two methods?

It seems to me that google-chrome and gnome-terminal changes more obviously from /etc/fonts/.

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The difference is the two different font configuration systems:

  • fontconfig - which allows fine-grained control over font settings, per-font customization etc... via config files like /etc/fonts/conf.d/* or ~/.config/fontconfig/fonts.conf

versus

  • XSettings - used by DE (read gtk) and configurable via user-friendly GUI tools (like gsettings, gnome-tweak-tool etc.), with limited configuration options (global settings, i.e. no font specific options)

The choice to follow fontconfig settings or XSettings is implementation specific, e.g. Epiphany - a gtk app based on webkitgtk - when rendering webpages uses fontconfig settings because webkitgtk devs decided to follow fontconfig settings and ignore XSettings.

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