Hi France,
finally some feedback (this year turns out to be even more packed than 2012).
I could not find how to set the UPDINDEX option to true() in the BaseX Gui. I also looked in .basexgui.
Some time ago, we decided to wait with the visual integration of the flag until UPDINDEX also works for the database statistics (name, path indexes) and the full-text index. The fastest option is to switch to the command input mode and type "SET UPDINDEX ON" once before creating new databases (or, once typed, retrieving it from the command history).
Best, Christian