We are seeing two issues when using Gradle 3.1 with the Jigsaw EA builds:

• Exception is:
  java.lang.ExceptionInInitializerError
  at org.gradle.initialization.DefaultClassLoaderRegistry.restrictToGradleApi(DefaultClassLoaderRegistry.java:48)
  at org.gradle.initialization.DefaultClassLoaderRegistry.<init>(DefaultClassLoaderRegistry.java:31)
  at org.gradle.internal.service.scopes.GlobalScopeServices.createClassLoaderRegistry(GlobalScopeServices.java:208)
  :
  Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected java.lang.Package[] java.lang.ClassLoader.getPackages() accessible: module java.base does not "exports private java.lang" to unnamed module @14f9390f
  at java.base/jdk.internal.reflect.Reflection.throwInaccessibleObjectException(Reflection.java:414)
  at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:198)
  at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:192)
  at java.base/java.lang.reflect.Method.setAccessible(Method.java:186)
  at org.gradle.internal.reflect.JavaMethod.<init>(JavaMethod.java:34)
  at org.gradle.internal.reflect.JavaMethod.<init>(JavaMethod.java:38)
  at org.gradle.internal.reflect.JavaReflectionUtil.method(JavaReflectionUtil.java:224)
  at org.gradle.internal.classloader.FilteringClassLoader.<clinit>(FilteringClassLoader.java:48)
  ... 39 more

This one can be worked around by running Gradle with `--add-exports-private java.base/java.lang=ALL-UNNAMED`.

The second one is uglier:

• Exception is:
  net.rubygrapefruit.platform.NativeException: Unable to get mutable environment variable map.
  at net.rubygrapefruit.platform.internal.WrapperProcess.getEnv(WrapperProcess.java:113)
  at net.rubygrapefruit.platform.internal.WrapperProcess.removeEnvInternal(WrapperProcess.java:91)
  at net.rubygrapefruit.platform.internal.WrapperProcess.setEnvironmentVariable(WrapperProcess.java:82)
  :
  Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.util.Map java.util.Collections$UnmodifiableMap.m accessible: module java.base does not "exports private java.util" to unnamed module @3bf9ce3e
  at java.base/jdk.internal.reflect.Reflection.throwInaccessibleObjectException(Reflection.java:414)
  at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:198)
  at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:171)
  at java.base/java.lang.reflect.Field.setAccessible(Field.java:165)
  at net.rubygrapefruit.platform.internal.WrapperProcess.getEnv(WrapperProcess.java:110)
  ... 17 more

where it should be possible to workaround with `--add-exports-private java.base/java.util=ALL-UNNAMED`, assuming there is a way to get this option into the command line of the launched VM.

There was a discussion on jigsaw-dev about this recently:
http://mail.openjdk.java.net/pipermail/jigsaw-dev/2016-October/009551.html

As announced on the Gradle blog we are planning to completely migrate issues from JIRA to GitHub.

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We look forward to collaborating with you more closely on GitHub. Thank you for your contribution to Gradle!

I think this issue is very high priority as there are many developers trying to use Gradle with JDK 9 and running into problems. The JavaFX build is one one example. There are also Oracle products trying to use Gradle with JDK 9 and running into the issues in this JIRA.

gradle/gradle#890 is going to be used to track all Jigsaw runtime related work for Gradle. We encourage you to subscribe to that issue.