Thanks. This is not really ideal though.
Isn't there a way to instead add the /media root directory so that I could keep 
my file paths identical to my system ?
I'm also not fond of using the flatpak because it would mess with all our 
scripts and most likely require to update them all with rather ugly commands 
like:

/usr/bin/flatpak run --branch=stable --arch=x86_64 --command=pto_gen 
--file-forwarding net.sourceforge.Hugin @@ %F @@

instead of:

pto_gen %F

I can't even add functions in bashrc to make the regular names of programs work 
in order to keep my scripts untouched because it doesn't deal with the 
multiline arguments present in my scripts.

Basically flatpak seems like a no-go for us (our small company), or at least we 
much prefer having benine error messages bother us. But it would sure be neat 
to find a somewhat easy way to make them disappear permanently.

Debian being one of the most popular and stable distros, I'm surprised not to 
find more messages about this issue, as I tried Hugin on a fresh Debian 12 
install and this error appears immediately.

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