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After reloading from disk, and seeing a lack of builds, took a heap dump with jmap and analyzed in the NetBeans profiler. There are indeed two FreeStyleProject instances with the same name. The second is the reloaded one, but the old one is still there; GC root reference analysis confirms my suspicions:
this - value: hudson.model.FreeStyleProject #1 <- myProject - class: com.sonyericsson.hudson.plugins.gerrit.trigger.hudsontrigger.GerritTrigger, value: hudson.model.FreeStyleProject #1 <- [2] - class: java.lang.Object[], value: com.sonyericsson.hudson.plugins.gerrit.trigger.hudsontrigger.GerritTrigger #1 <- array - class: java.util.concurrent.CopyOnWriteArrayList, value: java.lang.Object[] #44424 <- al - class: java.util.concurrent.CopyOnWriteArraySet, value: java.util.concurrent.CopyOnWriteArrayList #137 <- gerritEventListeners - class: com.sonyericsson.hudson.plugins.gerrit.trigger.GerritHandlerLifecycle, value: java.util.concurrent.CopyOnWriteArraySet #3 <- coordinator (thread object) - class: com.sonymobile.tools.gerrit.gerritevents.workers.EventThread, value: com.sonyericsson.hudson.plugins.gerrit.trigger.GerritHandlerLifecycle #1