// merge b1Tip and b2Tip and update refs/heads/b1 to the merge commit
Merger merger = MergeStrategy.SIMPLE_TWO_WAY_IN_CORE.newMerger(repo);
merger.merge(b1Tip, b2Tip);
CommitBuilder cb = tr.commit();
cb.parent(b1Tip).parent(b2Tip);
cb.setTopLevelTree(merger.getResultTreeId());
RevCommit mergeCommit = cb.create();
RefUpdate u = repo.updateRef("refs/heads/b1");
u.setNewObjectId(mergeCommit);
u.update();