It seems to me that you (and others probably) are violating Geany's non-reentrancy. It is not written to have operations happen in any way other than running to completion. Having something happen on another thread/mainloop while Geany is waiting for something will leave Geany stranded if that operation consumes the input that was meant for Geany. Thats why almost all popups and dialogs are modal, that stops the user causing something else to happen, but that doesn't stop plugins and sometimes even Geany itself doing it and breaking code that isn't written to handle it.

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