Found one Java-level deadlock:
    =============================
    "Handling POST /jenkins/html5-notifier-plugin/list from 192.168.1.181 : RequestHandlerThread[#40]":
      waiting to lock monitor 0x00007fc92c746878 (object 0x000000011c3abc30, a hudson.ExtensionList$Lock),
      which is held by "GitTool.onLoaded"
    "GitTool.onLoaded":
      waiting to lock monitor 0x00007fc92d3aa448 (object 0x000000011ce04750, a hudson.DescriptorExtensionList),
      which is held by "UpdateCenter.init"
    "UpdateCenter.init":
      waiting to lock monitor 0x00007fc92c746878 (object 0x000000011c3abc30, a hudson.ExtensionList$Lock),
      which is held by "GitTool.onLoaded"