- find where BaseX is really getting its config files ($HOME in my case); http://docs.basex.org/wiki/Configuration#Configuration_Files says "Q{org.basex.util.Prop}USERHOME()" which is exceedingly helpful!
- add, to .basex (NOT .basexgui) AFTER # Local Options the necessary config switch
- the config switch is "ARCHIVENAME = true"
- restart BaseX and go to recreate the DB and you'll see a ticky-box option for "add the archive name to the path"
This gets me the behaviour I was expecting would happen, but I'm still curious if there's a way to get the archive name back in the default case, because it does look like BaseX is in no way confused about which of those identically named files belong together.
Thanks!
Graydon