Recently I face error messages in a Provision script which updates Jenkins plugins.

It seems to happen when it tries to restarts Jenkins via CLI:

java -jar -s <url>/jenkins/ restart --username <Jenkins account with admin permissions> --password <password>

This call produces the following error message (though Jenkins restarts).

ERROR: Unexpected exception occurred while performing restart command.
java.lang.NullPointerException
        at jenkins.model.Jenkins.doRestart(Jenkins.java:4121)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at hudson.cli.declarative.MethodBinder.call(MethodBinder.java:114)
        at hudson.cli.declarative.CLIRegisterer$1.main(CLIRegisterer.java:224)
        at hudson.cli.CLIAction$PlainCliEndpointResponse$1.run(CLIAction.java:221)
        at jenkins.util.FullDuplexHttpService.download(FullDuplexHttpService.java:111)
        at jenkins.util.FullDuplexHttpService$Response.generateResponse(FullDuplexHttpService.java:171)
        at org.kohsuke.stapler.HttpResponseRenderer$Default.handleHttpResponse(HttpResponseRenderer.java:124)
        at org.kohsuke.stapler.HttpResponseRenderer$Default.generateResponse(HttpResponseRenderer.java:69)
        at org.kohsuke.stapler.Function.renderResponse(Function.java:136)
        at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:676)
        at org.kohsuke.stapler.Stapler.invoke(Stapler.java:845)
        at org.kohsuke.stapler.MetaClass$10.dispatch(MetaClass.java:374)
        at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:715)
        at org.kohsuke.stapler.Stapler.invoke(Stapler.java:845)
        at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
        at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:135)
        at com.smartcodeltd.jenkinsci.plugin.assetbundler.filters.LessCSS.doFilter(LessCSS.java:47)
        at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
        at hudson.plugins.scm_sync_configuration.extensions.ScmSyncConfigurationFilter$1.call(ScmSyncConfigurationFilter.java:49)
        at hudson.plugins.scm_sync_configuration.extensions.ScmSyncConfigurationFilter$1.call(ScmSyncConfigurationFilter.java:44)
        at hudson.plugins.scm_sync_configuration.ScmSyncConfigurationDataProvider.provideRequestDuring(ScmSyncConfigurationDataProvider.java:106)
        at hudson.plugins.scm_sync_configuration.extensions.ScmSyncConfigurationFilter.doFilter(ScmSyncConfigurationFilter.java:44)
        at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
        at hudson.plugins.greenballs.GreenBallFilter.doFilter(GreenBallFilter.java:59)
        at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
        at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:138)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at hudson.cli.CliCrumbExclusion.process(CliCrumbExclusion.java:47)
        at hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:58)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
        at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:135)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:92)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
        at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
        at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
        at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:90)
        at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:171)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:82)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:614)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:509)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1104)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1520)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1476)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:745)