I have it solved. The problem was that my jenkins directory was called "jenkins" and the jenkins.war file wanted to expand into the same place. Moving my jenkins to the default ".jenkins" kept its data separate from the extraction of the latest .war and it's all back again.
Interesting that the problem didn't occur on previous updates. -- You received this message because you are subscribed to the Google Groups "Jenkins Users" group. To unsubscribe from this group and stop receiving emails from it, send an email to jenkinsci-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
