Merge branch 'stable-6.6' into stable-6.7

* stable-6.6:
  Silence API warnings
  Make sure ref to prune is in packed refs
  Checkout: better directory handling

Change-Id: Id3b01c7a583d45b4e67e3f993006a5646f77a41d

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
Simple merge