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I could imagine that for instance ProjectOrganizer could be the problem if you let it index some huge project directory or the whole home directory but if you say the same problem persists when it's disabled, it must be something else then.
Do you have some big file open for instance? When you open Activity Monitor of macOS, do you see some big disk activity when you switch to the Disk tab? Is it the Geany process that consumes those 100% CPU or some other process too? Do you see some suspicious messages in the Console macOS application (the one for viewing logs)?
One other thing you could try is to rename the ~/.config/geany directory to something else (when Geany isn't open) so when you launch Geany it creates new configuration files in case something is wrong with your configuration.
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