To reproduce create manifest.txt with content
Multi-release: true
then create jar
$jar cfm test.jar manifest.txt .
java.util.jar.JarFile.isMultiRelease will return true for the jar.
Comments
A Mr.JAR is identified by the manifest main attribute:
Multi-Release: true
A developer can, if they want, bypass the specific support for multi-release (including validation) and assemble in this manner (with or without explicit versioned directories). I would not recommend this approach but i don't think we should disallow it.