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Follow up on https://git.eclipse.org/r/#/c/53827/16. Two tests were added : testCheckoutPathesDeletesFile testCheckoutPathesReplacesFileByFolder which shows that jgit has issues while checking out paths from another branch. testCheckoutPathesReplacesFileByFolder problem is in the CheckoutCommand.checkoutPaths(). It doesn't use DirCacheCheckout but tries to manipulate the working tree directly via checkoutPathsFromIndex() and this one doesn't use the "side" branch information. Since the second test is similar, I expect it also fails in same way.
New Gerrit change created: https://git.eclipse.org/r/57664