To uninstall properly, go back in the *geany-plugins* directory you cloned, then run `sudo make uninstall`. Then, to get back the Ubuntu version of pairtaghighliter (if you want it), do `sudo apt-get install --reinstall geany-plugin-pairtaghighlighter`. Then you can safely remove the *geany-plugins* directory and the packages you installed to build it (at least *libtool* and *libgtk2.0-dev*, but you might know which ones you had to install and which ones you already had).
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