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The App Store version of Ulysses doesn't contain a trial bar. Is it possible that you're still running the demo app? The Mac App Store version should have been installed directly to your Applications folder -- if not, please delete the Ulysses.app from there or move it to somewhere else and then re-download Ulysses via the App Store.
As far as I'm aware, the Mac App Store doesn't replace existing files in the /Applications folder (we don't have any influence on this). Thus, if the Ulysses demo was in /Applications, it was not replaced upon purchasing Ulysses from the App Store.