Fix StashApply regarding handling of untracked files

Fix StashApply regarding handling of untracked files

There was a bug regarding how JGit handled untracked files when applying
a stash. Problem was that untracked files are applied by doing a merge
of HEAD and untrackedFiles commit with a merge base of the stashed HEAD.
That's wrong because the untrackedFiles commit has no parent and
contains only the untracked files. Using stashed HEAD as merge base
leads to unneccessary conflicts on files not event included in the
untrackedFiles commit.

Imagine this graph directly before you want to apply a stash which was
based on 0. You want to apply the stash on current HEAD commit 5.

  5 (HEAD,master)
 /
0---+
 \   \
  1---3 (WIP on master)
     /
    2 (untracked files on master)

Imagine for a specific (tracked) file f
- commit 0 contains X
- HEAD contains Y
- commit 2 (the untracked files) does not contain file f

A merge of 2 and 5 with a merge base of 0 leads to a conflict. The 5
commit wants to modify the file and the 2 commit wants to delete the
file -> conflict.

If no merge base is set then the semantic is correct.

Thanks to Bow for finding this bug and providing the test case.

Bug: 485467
Change-Id: I453fa6ec337f81b2a52c4f51f23044faeec409e6
Also-by: Bow Ruggeri <bow@bow.net>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>