Do not handle "merged" files twice when JGit stages them

In some cases, JGit will stage the files that are "in-sync" directly
when walking over them instead of leaving this decision to the merger.
In such cases, EMF Compare's handling of files through the logical
model merging creates duplicate entries in the DirCache for stage 0.

Bug: 535200
Change-Id: I66e62cef3425289e384a02dcdcc8a2c1349d0400
1 file changed