Merge branch 'stable-4.3' into stable-4.4

* stable-4.3:
  Fix computation of id in WorkingTreeIterator with autocrlf and
    smudging
  Prepare 4.3.2-SNAPSHOT builds
  JGit v4.3.1.201605051710-r
  Scan loose ref before packed in case gc about to remove the loose
  Fix possible NPEs when reporting transport errors
  Fix calling of clean/smudge filters from Checkout,MergeCommands
  Fix ApplyCommand when result of patch is an empty file

Change-Id: I829f06699f6670e519d04c927bdba4b82df29199
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>