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or would they share config files or other resources?
Running Geany with -c ../config means it uses a separate config directory from your home one, and its inside the geany-git tree so it goes away with that tree. All Geany resources are referenced to prefix, and the one in geany-git has that as its prefix, so doesn't use any of your system geany resources. Obviously they share system libraries which is what we want to test. You can keep the new version around as long as you want of course, just cd geany-git/bin; ./geany -c ../config to run it again. Note the ./ when running the separate Geany, essential, if you forget it will run the system Geany.
Agree there are many moving parts, but you need to try enough combinations to identify the source of the issue, maybe keep a table:
| copy from | paste to | result |
|---|---|---|
| wayland Geany | X11 urxvt | fail |
| xwayland Geany | X11 urxvt | pass |
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