A related wish, UIBuilder will often save files that weren't modified during the session. I usually get eq2ui_fonts.xml, eq2ui_ime.xml, eq2ui_mainhud_guild.xml, eq2ui_mainhud_help.xml, eq2ui_mainhud_quantityselector.xml, eq2ui_mainhud_quickbar.xml, and eq2ui_popup_usagealarm.xml. Having it not do that would be nice.
(Unless it's something I did wrong, but I can't imagine what it would've been. Copied eq2ui.xml from Default, copied entire contents of currently applied custom UI folder, opened UIBuilder, clicked File -> Save, Closed UIBuilder. Poof, new files in my working folder.)