Don't raise checkout conflict for file missing in working tree

Don't raise checkout conflict for file missing in working tree

During a checkout we want to prevent to overwrite unsaved local file
content. Jgit was therefore checking whether the file to overwrite is
dirty or missing and would raise a conflict if this was the case. That
was wrong. It should only check if the file is dirty. It's ok to
"overwrite" a missing/non-existing file.

Change-Id: I63c3a94f663c87f09170fdf8b1b1bf4ed5246fc5
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>