Not sure what's going on there. One suggestion is to not use /usr/local prefix, sooner or later you're going to mess up your system like that (makes you use root and contains other important stuff). Also recommend to use a clean config dir for testing to make sure other settings aren't getting in the way.

Example of building Geany & Geany-Plugins:

$ export PREFIX=$HOME/local-geany
$ cd geany
$ mkdir -p ../geany-build
$ cd ../geany-build
$ ../geany/configure --prefix=$PREFIX
$ make install
$ cd ../geany-plugins
$ mkdir -p ../geany-plugins-build
$ cd ../geany-plugins-build
$ ../geany-plugins/configure --prefix=$PREFIX --with-geany-libdir=$PREFIX/lib
$ make install
$ $PREFIX/bin/geany -v -c /tmp/testing

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