See this page (https://docs.gocd.org/current/installation/install/server/windows.html#overriding-default-startup-arguments-and-environment) for details on setting up system properties.
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You shouldn't remove the "#" before the "#include". Though the rest of the lines prefixed with a "#" are comments, in the case of the include directive, it is: "#include", as you can see here: https://wrapper.tanukisoftware.com/doc/english/props-cascading.html
"Runtime Information": { "Name": "4808@SEAPRODMGMT01", "Uptime": 314474, "Uptime (in Time Format)": "[About 0 hours, 5 minutes, 14 seconds]", "Spec Name": "Java Virtual Machine Specification", "Spec Vendor": "Oracle Corporation", "Spec Version": "1.8", "Input Arguments": [ "-Xms512m", "-Xmx1024m", "-DreservedForFuture.6", "-XX:MaxMetaspaceSize\u003d256m", "-Duser.language\u003den", "-Duser.country\u003dUS", "-Dcruise.config.dir\u003de:\\Go\\Server\\config", "-Dcruise.config.file\u003de:\\Go\\Server\\config\\cruise-config.xml", "-DreservedForFuture.1", "-DreservedForFuture.2", "-DJAVA_SYS_MON_TEMP_DIR\u003de:\\Go\\Server\\tmp", "-Dno_debugging", "-Dno_gc_logging", "-DreservedForFuture.4", "-DreservedForFuture.5", "-Dgo.config.repo.gc.periodic\u003dY", "-Dgo.config.repo.gc.cron\u003d0 0 3 * * ?", "-Dfile.encoding\u003dCp1252", "-Djava.library.path\u003dlib", "-Dwrapper.key\u003dw22wjMY8wrExwALygeNX6010A04i0LT0", "-Dwrapper.port\u003d32000", "-Dwrapper.jvm.port.min\u003d31000", "-Dwrapper.jvm.port.max\u003d31999", "-Dwrapper.pid\u003d5000", "-Dwrapper.version\u003d3.5.30-st", "-Dwrapper.native_library\u003dwrapper", "-Dwrapper.arch\u003dx86", "-Dwrapper.service\u003dTRUE", "-Dwrapper.cpu.timeout\u003d10", "-Dwrapper.jvmid\u003d1", "-Dwrapper.lang.domain\u003dwrapper", "-Dwrapper.lang.folder\u003d../lang" ], "System Properties": { "JAVA_SYS_MON_TEMP_DIR": "e:\\Go\\Server\\tmp", "awt.toolkit": "sun.awt.windows.WToolkit", "com.microsoft.tfs.jni.native.base-directory": "e:\\Go\\Server\\data\\tfs-sdk\\tfssdk\\native", "cruise.config.dir": "e:\\Go\\Server\\config", "cruise.config.file": "e:\\Go\\Server\\config\\cruise-config.xml", "file.encoding": "Cp1252", "file.encoding.pkg": "sun.io", "file.separator": "\\", "go.config.repo.gc.cron": "0 0 3 * * ?", "go.config.repo.gc.periodic": "Y", "java.awt.graphicsenv": "sun.awt.Win32GraphicsEnvironment",
"-Dgo.config.repo.gc.periodic\u003dY", "-Dgo.config.repo.gc.cron\u003d0 0 7 1/1 \\* \\?",
Which makes me think I've got an issue with escape characters, as yours looks like a real cron expression.
I followed the doc's with their comments on escaping special characters
(added to /etc/defaults/go-server):
GO_SERVER_SYSTEM_PROPERTIES="$GO_SERVER_SYSTEM_PROPERTIES -Dgo.config.repo.gc.periodic=Y -Dgo.config.repo.gc.cron='0 0 7 1/1 \* \?'"
Since I raised this issue we've actually switched to a Linux server so the mechanism is slightly different. When I view my support page I see:"-Dgo.config.repo.gc.periodic\u003dY", "-Dgo.config.repo.gc.cron\u003d0 0 7 1/1 \\* \\?",