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Could you be more specific about what you're asking for?
If you want to use Calibre as a program launcher, it's possible although there are better solutions out there. You can drag a shortcut into Calibre and it will be entered in the database as a book entry (despite the fact that it's not a book). When you double-click on it, it will execute the program the shortcut points to.
If instead you want to open books in your library with external programs, either disable them in the list of formats Calibre uses its internal reader for, or get the Open With plugin, which you can set up to use as many external programs as you want.
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