As I reply everyone raising this "bug", get a properly configured `sudo`. Even though I don't recommend using Geany as root, I can just fine run `sudo geany` on my Debian machine and it works flawlessly (as far as I can tell without doing it daily, though), whether or not I have other Geanys running. It properly uses */root/.config/geany* as the configuration directory.
*Anything* that would lead to another user (including root) to writing in a user's home directory should be avoided. If you *did* write there as root, the user would be left with root-owned file in his home, files he couldn't modify. That's not a good thing.
And while I don't want special code for handling `sudo` use, I don't think any is needed: proof being I can use `sudo` just fine on my machine. Yes, Debian does have `Defaults env_reset`.
If you *really* want us to change something, you'll need to detail why you'd need inheriting the environment (including `HOME` and `XDG_*`, and possibly other) in your sudo session, and what you'd want us to do to fix it (by that I mean actual changes, not "fix it").
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If "many other GUI tools" work, it might be for a number of reasons, one possibly being that they use DBus (anything using *dconf* comes to mind), which may or may not use `$USER` rather than `$HOME`/`$XDG_*`. Or other special handling. Or possibly simply not have to do any IPC and happily mess up your user's home directory. If really other tools to something meaningful and it's not a hack, maybe it could be a basis for proposing a change.
Out of curiosity, do you have root-owned stuff in your dotfiles? `(cd && find -path './.*' -user root)`
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*I'm not closing it just now, but I still do consider this invalid at least for the moment*
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