builtin/merge.c contains this important requirement for merge strategies:
        /*
         * At this point, we need a real merge.  No matter what strategy
         * we use, it would operate on the index, possibly affecting the
         * working tree, and when resolved cleanly, have the desired
         * tree in the index -- this means that the index must be in
         * sync with the head commit.  The strategies are responsible
         * to ensure this.
         */

merge-recursive does not do this check directly, instead it relies on
unpack_trees() to do it.  However, merge_trees() has a special check for
the merge branch exactly matching the merge base; when it detects that
situation, it returns early without calling unpack_trees(), because it
knows that the HEAD commit already has the correct result.  Unfortunately,
it didn't check that the index matched HEAD, so after it returned, the
outer logic ended up creating a merge commit that included something
other than HEAD.

Signed-off-by: Elijah Newren <new...@gmail.com>
---
 merge-recursive.c                        | 7 +++++++
 t/t6044-merge-unrelated-index-changes.sh | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/merge-recursive.c b/merge-recursive.c
index 2ecf495cc2..780f81a8bd 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -1952,6 +1952,13 @@ int merge_trees(struct merge_options *o,
        }
 
        if (oid_eq(&common->object.oid, &merge->object.oid)) {
+               struct strbuf sb = STRBUF_INIT;
+
+               if (index_has_changes(&sb)) {
+                       err(o, _("Dirty index: cannot merge (dirty: %s)"),
+                           sb.buf);
+                       return 0;
+               }
                output(o, 0, _("Already up to date!"));
                *result = head;
                return 1;
diff --git a/t/t6044-merge-unrelated-index-changes.sh 
b/t/t6044-merge-unrelated-index-changes.sh
index 5e472be92b..23b86fb977 100755
--- a/t/t6044-merge-unrelated-index-changes.sh
+++ b/t/t6044-merge-unrelated-index-changes.sh
@@ -112,7 +112,7 @@ test_expect_success 'recursive' '
        test_must_fail git merge -s recursive C^0
 '
 
-test_expect_failure 'recursive, when merge branch matches merge base' '
+test_expect_success 'recursive, when merge branch matches merge base' '
        git reset --hard &&
        git checkout B^0 &&
 
-- 
2.15.1.436.g63a861020b

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