For searching in files, ProjectOrganizer just uses Geany's standard search using grep and there's no API in Geany that would allow ProjectOrganizer pass the ignored files/directories to Geany. In fact, Geany itself doesn't support patterns for excluded files/directories - the reason is that --exclude and --exclude-dir parameters of grep aren't present in older versions of grep and it's not guaranteed they would work.

There's nothing that could be done in the plugin to address this issue. Plugins cannot add extra parameters to grep - it's done by Geany when using the "Project" settings in the "Find in Files" dialog and when patterns are entered in the Geany's part of the Project settings.

As a workaround I'd suggest selecting "Extra Options" in the Find in Files dialog and entering --exclude-dir=pattern where pattern corresponds to the directories you want to ignore.

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