I cleared the folders and ran the ./install file which created fresh copies of the files in ~/.config/geany/filedefs and colorschemes.

Here is the output from the file:

23:43:15: Gtk WARNING : Unable to locate theme engine in module_path: "pixmap", 23:43:15: Gtk WARNING : Unable to locate theme engine in module_path: "pixmap", 23:43:15: Gtk WARNING : Unable to locate theme engine in module_path: "pixmap", 23:43:15: Gtk WARNING : Unable to locate theme engine in module_path: "pixmap", 23:43:15: Geany INFO : Geany 0.21, en_US.UTF-8 23:43:15: Geany INFO : GTK 2.24.6, GLib 2.30.0 23:43:15: Geany INFO : System data dir: /usr/local/share/geany 23:43:15: Geany INFO : User config dir: /home/noah/.config/geany 23:43:16: Geany INFO : Added filetype Cython (52). 23:43:16: Geany INFO : Added filetype Scala (53). 23:43:16: Geany INFO : Added filetype Genie (54). 23:43:16: Geany INFO : /var/www/tony/modules/kacela/vendor/Gacela/library/Gacela/Mapper/Mapper.php : PHP (UTF-8) 23:43:16: Geany INFO : Loaded /usr/local/share/geany/php.tags (PHP), 2338 tag(s). 23:43:16: LIBDBUSMENU-GTK CRITICAL : watch_submenu: assertion `GTK_IS_MENU_SHELL(menu)' failed