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home config file in ~/.vimrc (this works everywhere except Geany)
global config file in /etc/vimrc (this works everywhere except Geany)
It is almost certain that these are not hard coded paths, they will use environment variables. Thats why I suggested you echo them in the VTE to be sure those variables are set properly.
You didn't answer the question of how you were running Geany, menu or terminal?
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