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To get WindowBuilder in Eclipse to work I had to install some dependencies. One of them seems to have changed the font everywhere, even in the terminals. It somehow looks like KDE fonts.

These are the ones that I installed:

  • libiw-dev
  • libhunspell-1.3-0
  • libasound2-dev
  • libnotify-dev
  • libdbus-glib-1-dev
  • libgtk2.0-dev
  • libgtk2.0-0
  • gtk2-engines
  • libidl-dev
  • libhunspell-dev
  • libstdc++6-4.4-dev
  • pango-graphite

Which one could be the one that changed it?

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It's pango-graphite. Pango is a library for layout and rendering of text, with an emphasis on internationalization. From the pango-graphite package description:

SILGraphite is a system that can be used to create and use "smart fonts" capable of displaying writing systems with various complex behaviors, such as: contextual shaping, ligatures, reordering, split glyphs, bidirectionality, stacking diacritics and complex positioning.

For more details see this bug report: Pango-graphite changes default UI font in Ubuntu 13.04.

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