final MergeCommand mc = git.merge();
try {
    for (final ObjectId head : git.getRepository().readMergeHeads()) {
        mc.include(head);
    }
} catch (final NoWorkTreeException e1) {
    // TODO Auto-generated catch block
    e1.printStackTrace();
} catch (final IOException e1) {
    // TODO Auto-generated catch block
    e1.printStackTrace();
}
mc.setStrategy(MergeStrategy.THEIRS);
try {
    final MergeResult mr = mc.call();
} catch(... lots of cases){}

+ git init --bare central
Initialized empty Git repository in /tmp/central/
+ git clone central/ bob
Cloning into 'bob'...
warning: You appear to have cloned an empty repository.
done.
+ cd bob/
+ echo -e '1\n2\n3'
+ echo -e '1\n2\n3'
+ git add .
+ git commit -m initial
[master (root-commit) 22cc5a7] initial
 2 files changed, 6 insertions(+)
 create mode 100644 common1
 create mode 100644 common2
+ git push
Counting objects: 3, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (3/3), 225 bytes | 0 bytes/s, done.
Total 3 (delta 0), reused 0 (delta 0)
To /tmp/central/
 * [new branch]      master -> master
+ cd ..
+ git clone central/ dave
Cloning into 'dave'...
done.
+ cd bob/
+ echo -e '1bob\n2\n3'
+ echo -e '1\n2bob\n3'
+ echo bobsContent
+ git add .
+ git commit -m bobsChanges
[master 4fec0dd] bobsChanges
 3 files changed, 3 insertions(+), 2 deletions(-)
 create mode 100644 bobsFile
+ git push
Counting objects: 5, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (5/5), 353 bytes | 0 bytes/s, done.
Total 5 (delta 0), reused 0 (delta 0)
To /tmp/central/
   22cc5a7..4fec0dd  master -> master
+ cd ../dave
+ echo -e '1\n2\n3dave'
+ echo -e '1\n2dave\n3'
+ echo davesContent
+ git add .
+ git commit -m davesChanges
[master b5118ee] davesChanges
 3 files changed, 3 insertions(+), 2 deletions(-)
 create mode 100644 davesFile
+ git pull
remote: Counting objects: 5, done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 5 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.
From /tmp/central
   22cc5a7..4fec0dd  master     -> origin/master
Auto-merging common2
CONFLICT (content): Merge conflict in common2
Auto-merging common1
Automatic merge failed; fix conflicts and then commit the result.
+ git merge -s ours FETCH_HEAD
error: merge is not possible because you have unmerged files.
hint: Fix them up in the work tree, and then use 'git add/rm <file>'
hint: as appropriate to mark resolution and make a commit.
fatal: Exiting because of an unresolved conflict.