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Ok, problem solved, the machine I am using temporarily had another Geany installed, explicit executable path fixed this :-)
I remember having this problem when switching between meson build and autotools build - each of them installs geany.so to a different location - autotools to /usr/local/lib and meson to /usr/local/lib/aarch64-linux-gnu and I think the latter one takes precedence. If there were a way to unify this behavior, it would be great to avoid similar problems.
Back to the reported problem, another possibility could have been that you had some old config files in the config directory which contained the #~ - these legacy config files will stay as they are.
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