I have been able to reproduce this error on a porterbox. Curiously the
file reported as missing is actually there after the build:

(sid_armhf-dchroot)ebourg@asachi:~/groovy2$ ls -l
buildSrc/target/classes/main/JavadocFixTool.class
-rw-r--r-- 1 ebourg Debian 8188 Nov  9 17:32
buildSrc/target/classes/main/JavadocFixTool.class

I wonder if this could be an issue with the native layer checking the
existence of the file, either in jruby or gradle according to the root
exception:

java.lang.UnsupportedOperationException: No such file or directory -
/home/ebourg/groovy2/buildSrc/target/classes/main/JavadocFixTool.class
        at
org.gradle.internal.nativeplatform.filesystem.PosixUtil$POSIXHandlerImpl.error(PosixUtil.java:38)
        at org.jruby.ext.posix.JavaLibCHelper.stat(JavaLibCHelper.java:186)
        at org.jruby.ext.posix.JavaPOSIX.stat(JavaPOSIX.java:223)
        at org.jruby.ext.posix.LazyPOSIX.stat(LazyPOSIX.java:227)
        at
org.gradle.internal.nativeplatform.filesystem.LibCStat.getUnixMode(LibCStat.java:41)
        at
org.gradle.internal.nativeplatform.filesystem.GenericFileSystem.getUnixMode(GenericFileSystem.java:62)
        at
org.gradle.api.internal.file.DefaultFileTreeElement.getMode(DefaultFileTreeElement.java:66)
        at
org.gradle.api.internal.file.copy.MappingCopySpecVisitor$FileVisitDetailsImpl.getMode(MappingCopySpecVisitor.java:164)
        at
org.gradle.api.internal.file.archive.ZipCopySpecVisitor.visitFile(ZipCopySpecVisitor.java:56)

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