Hi,
I believe there is a usability flaw in Geany - opened documents' list is saved only if you exit the editor in 'traditional' way (by clicking exit button or so). It's completely lost, if the process's killed. This was irritating for me, as I tend not to close every program when shutting down, but rather push the 'shutdown' button and get them all killed - and get the list of opened documents lost. I believe I'm not the only one saving time on this, moreover, if your system hangs, you loose this list as well.
Anyway, this wasn't hard to fix - just calling *configuration_save() *upon opening or closing a file. Operation itself seems to be cheap (although it's rewriting a config completely, as I see) - noticed no performance issues on my 1 GB RAM netbook.
Sent you a pull request on GitHub.