Thanks again for reporting the issue. I put up this PR to exclude sun.misc.* from the MANIFEST.MF. #3091

I'll separately have a look at the issue where MANIFEST.MF was not the first file listed

It looks like that whatever is building the JAR file in shadowJar is not aware of that. When I extract the JAR file and then use 'jar -cvf' it will create the correct / expected JAR file with the MANIFEST.MF as first entry.
Keep in mind that for example java.util.jar.JarInputStream is not finding the MANIFEST.MF if it is not the first entry (new JarInputStream(ins).getManifest() will return null).

After some back and forth (I am not a gradle expect) I came up with this as a soluition (starting at line 143):

task extractWithoutGuava(type: Copy) {
from({ zipTree({ "build/libs/graphql-java-${project.version}.jar" }) }) {
exclude('/com/**')
}
into layout.buildDirectory.dir("extract")
}

task buildNewJar(type: Jar) {
from layout.buildDirectory.dir("extract")
archiveFileName = "graphql-java-tmp.jar"
destinationDirectory = file("${project.buildDir}/libs")
manifest {
from file("build/extract/META-INF/MANIFEST.MF")
}
doLast {
delete("build/libs/graphql-java-${project.version}.jar")
file("build/libs/graphql-java-tmp.jar").renameTo(file("build/libs/graphql-java-${project.version}.jar"))
}
}

shadowJar.finalizedBy extractWithoutGuava, buildNewJar

I created a PR for my 'fix': #3097

Thanks so much for the PR, I've merged it!