I can't follow your steps to reproduce there seems to be missing steps. I presume you built from nightly tarball to get a 1.39, unfortunately that doesn't say what the git was when you built it as it does for built from git (see below), 1.39 is still in development so things can change at any point.
I ran Geany:
(null): Geany INFO : Geany 1.39 (git >= b7558417), en_AU.UTF-8
(null): Geany INFO : GTK 3.24.20, GLib 2.64.6
(null): Geany INFO : OS: Linux Mint 20 (ulyana)
on a separate config ie geany -c /tmp/something
and did:
AFAIK thats the expected behaviour. If yours behaves differently can you post the values of the treeview_position
and geometry
from /tmp/something/session.conf
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