I don't think its neccessary to worry about disk IO unless its having an effect on performance, but since save only occurs when config data changes and that is when there is a major screen update (new document, close document etc) its not likely to be noticed. If it does cause performance issues, eg because the config file is on some slow remote filesystem then there is now an option to turn this saving off.
As for saving disk life, on my systems something in the OS writes to disk every few seconds (with no user apps open), so I doubt the Geany config saving will have a material effect on lifetime.
Only aggregating and only saving on focus loss is ok for user logout since it will be hard to invoke logout or shutdown without de-focussing geany, but it will not handle a crash though.
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