With the preferences restored, I've implemented remembering size and position for dialogs. Only two dialogs are affected for now, the toolbox (only position) and fill/stroke (size and position). Please test and report any problems. Finally, after this change is tested, I will copy the entire code over to all other dialogs.
Preferences are now saved in ~/.inkscape/preferences.xml, instead of simply ~/.inkscape/preferences. I think it's more logical this way.
A new signal was added, "shut_down". It is sent by the inkscape object before shutting down inkscape and before saving preferences, so that dialogs have the chance to write their status into the preferences. If anyone else needs to do some housekeeping before program shuts down, they may use this signal.
New shortcut: * for the star tool. By the way, the number of star rays was written in prefs, and this now works. Lots of other parameters need to be similarly written and restored. I will soon update the wiki page with instructions on how to handle this.