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It's unclear what the bug is: To be backwards compatible (and allow a smooth upgrade experience from former Hudson), Jenkins considers directories like '~/.hudson' to be valid default locations, and respects variables like 'HUDSON_HOME'.
If users upgraded to Hudson 2.x+, then cross-grade to Jenkins, it seems obvious that this will result in problems.
Given that the split has happened over three years ago, at most a handful of systems would profit from special handling of that.