[JENKINS-61694] - Update Groovy Init hooks to run after all job configurations are adapted

core/src/main/java/hudson/init/InitMilestone.java

@@ -106,14 +106,15 @@ public enum InitMilestone implements Milestone {
     JOB_LOADED("Loaded all jobs"),
 
     /**
-     * By this milestone, any job configuration is adapted or updated just in case any plugin needs to update former/old configurations or init scripts
+     * By this milestone, any job configuration is adapted or updated just in case any plugin needs to update former/old configurations.
+     * It does not include {@link hudson.init.impl.GroovyInitScript}s which get executed later
      * @since 2.220
      */
     JOB_CONFIG_ADAPTED("Configuration for all jobs updated"),
 
     /**
-     * The very last milestone
-     *
+     * The very last milestone.
+     * All executions should be completed by it, including {@link hudson.init.impl.GroovyInitScript}s.
      * This is used in {@link Initializer#before()} since annotations cannot have null as the default value.
      */
     COMPLETED("Completed initialization");

core/src/main/java/hudson/init/impl/GroovyInitScript.java

@@ -32,11 +32,12 @@ import static hudson.init.InitMilestone.*;
 
 /**
  * Run the initialization script, if it exists.
+ * It runs strictly after the initialization of other tasks during the last initialization milestone.
  * 
  * @author Kohsuke Kawaguchi
  */
 public class GroovyInitScript {
-    @Initializer(after=JOB_LOADED)
+    @Initializer(after=JOB_CONFIG_ADAPTED)
     public static void init(Jenkins j) {
         new GroovyHookScript("init", j.servletContext, j.getRootDir(), j.getPluginManager().uberClassLoader).run();
     }