Patch Set 3:

This is broken:

org.eclipse.jgit.core--All-Tests (Java 6)
org.eclipse.jgit.lib.WorkDirCheckout_ReadTreeTest
testDirectoryFileSimple(org.eclipse.jgit.lib.WorkDirCheckout_ReadTreeTest)
junit.framework.AssertionFailedError
	at junit.framework.Assert.fail(Assert.java:47)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at junit.framework.Assert.assertTrue(Assert.java:27)
	at org.eclipse.jgit.lib.ReadTreeTest.testDirectoryFileSimple(ReadTreeTest.java:277)


testCheckoutOutChanges(org.eclipse.jgit.lib.WorkDirCheckout_ReadTreeTest)
junit.framework.AssertionFailedError: unexpected content for path foo in index. Expected: <bar>
	at junit.framework.Assert.fail(Assert.java:47)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at org.eclipse.jgit.lib.ReadTreeTest.assertIndex(ReadTreeTest.java:674)
	at org.eclipse.jgit.lib.ReadTreeTest.testCheckoutOutChanges(ReadTreeTest.java:591)
	at