This is running under Sway, testing with Wayland native apps only (no xwayland).
When I first open a file in Geany, I can copy out of Geany and paste into another program by selecting and then middle clicking in the usual way. I can do that multiple times with different selections. If I then select something ("foo" for example) in the other program, I can middle click paste it into Geany. I can do this with multiple selections as well. All OK so far.
At this point if I select something in Geany ("bar" for example), I can no longer middle click paste it outside of Geany. I just get "foo" instead, even if I make sure to unselect "foo" in the other app before selecting "bar" in Geany. Middle click copy/paste within Geany works fine still. It also works fine within and between non-Geany applications. It is as if Geany is now using a different primary buffer than everything else.
Opening a new file in Geany (or closing and reopening an existing one) gets things working again temporarily.
I've tested this with Geany 1.36 and also the latest Master branch. I also tried applying the patch from here, but saw no difference: https://sourceforge.net/p/scintilla/bugs/2127/
I have mainly been using kitty (0.18.3) and firefox (78.3.0 esr) as the other applications. Sway is version 1.5-3. This is on Debian Bullseye. I also briefly tried to check if SciTe exhibits the same behavior, but middle click copy paste did not work at all there (at least to other programs, not sure if it worked within SciTe).
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