...Is there a case for uninstalling Oolite and updating/reinstalling Trunk?
Firts of all, let me reassure you that Oolite and Oolite-Trunk installations can live happily side by side.
However, they will both use (read AND write, if needed) whatever exists under
(e.g. logs, addons)
(e.g. snapshots, savegames)
(e.g. default game settings)
(e.g. game managed addons, cache)
Furthermore, the warnings, you get by oolite execution can be ignored. The game starts with no audio issues, right?
To uninstall a non-privileged (i.e. non system-wide) installation, such as yours, you can just delete the Oolite folder.
$rm -rf ~/GNUstep/Applications/Oolite/
For a more graceful removal, that gives a try to preserve post-installation user files, you can execute
This one will try to preserve some Oolite folders that could contain post installation user files. However, it will unconditionally delete folders such as
The same removal process stands for
In any case, and for the first run of your new installation, do not forget to flush the cache by holding the "Shift" key when starting Oolite (or Oolite-trunk).