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Discovered by visual inspection while tracking down an unrelated issue. Here's a simple test that illustrates the issue:
Joint testJoint = new Joint("testJoint");
Assert.assertTrue(testJoint.getInitialTransform().isIdentity());
Joint clone = Cloner.deepClone(testJoint);
clone.getInitialTransform().setScale(2f);
Assert.assertTrue(testJoint.getInitialTransform().isIdentity());The 2nd assertTrue() fails because testJoint and its clone share the same initial transform.
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