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BTW, I want to point out that having other-user-owned files in your homedir is not a problem specific to Geany, and is gonna cause more trouble (and possibly more subtle) than just this message. Think impossibility to save (or possibly even read) configuration or plain files, etc.
Check your homedir with e.g. find ~ '!' -user "$USER" (untested right now, but should be close enough): if you get any result, you might have issues with those files. You can limit that to ~/.config/ first if you have a lot of things in your homedir as s first indicator.
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