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I have changed the symlink /usr/share/dict/words to point to my own custom dictionary but it doesn't seem to affect anything.

Chromium and Abiword neither seem to use this dictionary.

Which appilications use words? Do I have to manually configure each application to use it? What is the point of having a system dictionary if applications are going to use their own anyway?

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Look for packages depending on that file/the package containing it... my (not minimal, but not full either) shows no installed packages depending on it. –  vonbrand Mar 4 '13 at 3:17
    
For Arch linux, no packages seem to depend on /usr/share/dict/words, which constitutes its own package, "community/words". pacman -Q -i words seems to indicate that GNU aspell uses it, but there's no package dependency. –  Bruce Ediger Mar 4 '13 at 4:12
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Two come to mind: both look from util-linux(man look and read description) and ispell (for the lookup) use that file. Most likely it has also other uses that I'm not aware of.

As to your other question (Chromium, Abiword etc)... Most distros nowadays use a wrapper lib called enchant for spell checking. enchant supports up to 8 back-ends that actually do the spell-check job (see home project page), hunspell (forked from myspell) and aspell being the most popular. You'll have to look into the particulars of your distro and get familiar with enchant and its backend(s)...

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