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The popup should be modal, nothing else should be able to steal focus. Almost all of Geany is written on the assumption that focus stealing, calls to Geany functions while other Geany functions are waiting for input and the like do not happen. They are likely to misbehave if unexpected things happen, like focus getting stolen from a modal dialog, by a plugin doing something at an unexpected moment (thats another of the recent Issues IIRC).
Fixing individual issues is going to be a game of whack a mole because almost all of Geany is not written to handle it, the whole thing needs to be carefully thought about, not just each individual bug swatted as it comes up when the timing happens to be wrong on someones system.
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