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Currently createAndSetDirectories() create ~/.freecol. It would be better to use locations defined in the XDG Base Directory Specification.
Paolo, if you are rewriting the directory code anyway, you could have a look at this issue.
What is planned now about FreeDesktop XDG basedir specification for FreeCol?
When last discussed on freecol-devel, we agreed to defer fixing this until the next major release.
As of git.f8f17f2 FreeCol should now be XDG compliant. Setting to Pending until next release.