Patch Set 2:

this breaks the egit core test RebaseOperationTest.testStopAndAbortOnConflict(), please fix that test

Rerun org.eclipse.egit.core.test.op.RebaseOperationTest.testStopAndAbortOnConflict
testStopAndAbortOnConflict(org.eclipse.egit.core.test.op.RebaseOperationTest)
org.eclipse.core.runtime.CoreException: Checkout conflict with file: Cannot delete file: .metadata
	at org.eclipse.egit.core.op.RebaseOperation$1.run(RebaseOperation.java:106)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1975)
	at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:1957)
	at org.eclipse.egit.core.op.RebaseOperation.execute(RebaseOperation.java:112)
	at org.eclipse.egit.core.test.op.RebaseOperationTest.testStopAndAbortOnConflict(RebaseOperationTest.java:182)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:31)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
	at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:49)
	at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390)
	at org.eclipse.pde.internal.junit.runtime.RemotePluginTestRunner.main(RemotePluginTestRunner.java:62)
	at org.eclipse.pde.internal.junit.runtime.CoreTestApplication.run(CoreTestApplication.java:23)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:369)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:619)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:574)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1407)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1383)
Caused by: org.eclipse.jgit.api.errors.JGitInternalException: Checkout conflict with file: Cannot delete file: .metadata
	at org.eclipse.jgit.api.RebaseCommand.call(RebaseCommand.java:200)
	at org.eclipse.egit.core.op.RebaseOperation$1.run(RebaseOperation.java:99)
	... 47 more
Caused by: org.eclipse.jgit.errors.CheckoutConflictException: Checkout conflict with file: Cannot delete file: .metadata
	at org.eclipse.jgit.dircache.DirCacheCheckout.cleanUpConflicts(DirCacheCheckout.java:805)
	at org.eclipse.jgit.dircache.DirCacheCheckout.checkout(DirCacheCheckout.java:398)
	at org.eclipse.jgit.api.RebaseCommand.abort(RebaseCommand.java:602)
	at org.eclipse.jgit.api.RebaseCommand.call(RebaseCommand.java:198)
	... 48 more