Merge branch 'sb/test-cherry-pick-submodule-getting-in-a-way'

The three-way merge performed by "git cherry-pick" was confused
when a new submodule was added in the meantime, which has been
fixed (or "papered over").

* sb/test-cherry-pick-submodule-getting-in-a-way:
merge-recursive: handle addition of submodule on our side of history
t/3512: demonstrate unrelated submodule/file conflict as cherry-pick failure

diff --combined merge-recursive.c
index 85b4e58478fad71ca754673777dc255922773b7f,9fb0b9f8fdfe12b58b5876a4984f4bf9a9f5c0fb..d00b274381e7fff7efd2b38f4328764105d9d7af
--- 1/merge-recursive.c
--- 2/merge-recursive.c
+++ b/merge-recursive.c
@@@ -540,8 -540,8 +540,8 @@@ static struct string_list *get_renames(
                return renames;
  
        diff_setup(&opts);
 -      DIFF_OPT_SET(&opts, RECURSIVE);
 -      DIFF_OPT_CLR(&opts, RENAME_EMPTY);
 +      opts.flags.recursive = 1;
 +      opts.flags.rename_empty = 0;
        opts.detect_rename = DIFF_DETECT_RENAME;
        opts.rename_limit = o->merge_rename_limit >= 0 ? o->merge_rename_limit :
                            o->diff_rename_limit >= 0 ? o->diff_rename_limit :
@@@ -1901,8 -1901,9 +1901,9 @@@ static int process_entry(struct merge_o
                        oid = b_oid;
                        conf = _("directory/file");
                }
-               if (dir_in_way(path, !o->call_depth,
-                              S_ISGITLINK(a_mode))) {
+               if (dir_in_way(path,
+                              !o->call_depth && !S_ISGITLINK(a_mode),
+                              0)) {
                        char *new_path = unique_path(o, path, add_branch);
                        clean_merge = 0;
                        output(o, 1, _("CONFLICT (%s): There is a directory with name %s in %s. "
@@@ -2162,7 -2163,7 +2163,7 @@@ int merge_recursive_generic(struct merg
                            struct commit **result)
  {
        int clean;
 -      struct lock_file *lock = xcalloc(1, sizeof(struct lock_file));
 +      struct lock_file lock = LOCK_INIT;
        struct commit *head_commit = get_ref(head, o->branch1);
        struct commit *next_commit = get_ref(merge, o->branch2);
        struct commit_list *ca = NULL;
@@@ -2178,14 -2179,14 +2179,14 @@@
                }
        }
  
 -      hold_locked_index(lock, LOCK_DIE_ON_ERROR);
 +      hold_locked_index(&lock, LOCK_DIE_ON_ERROR);
        clean = merge_recursive(o, head_commit, next_commit, ca,
                        result);
        if (clean < 0)
                return clean;
  
        if (active_cache_changed &&
 -          write_locked_index(&the_index, lock, COMMIT_LOCK))
 +          write_locked_index(&the_index, &lock, COMMIT_LOCK))
                return err(o, _("Unable to write index."));
  
        return clean ? 0 : 1;
@@@ -2201,7 -2202,6 +2202,7 @@@ static void merge_recursive_config(stru
  
  void init_merge_options(struct merge_options *o)
  {
 +      const char *merge_verbosity;
        memset(o, 0, sizeof(struct merge_options));
        o->verbosity = 2;
        o->buffer_output = 1;
@@@ -2210,9 -2210,9 +2211,9 @@@
        o->renormalize = 0;
        o->detect_rename = 1;
        merge_recursive_config(o);
 -      if (getenv("GIT_MERGE_VERBOSITY"))
 -              o->verbosity =
 -                      strtol(getenv("GIT_MERGE_VERBOSITY"), NULL, 10);
 +      merge_verbosity = getenv("GIT_MERGE_VERBOSITY");
 +      if (merge_verbosity)
 +              o->verbosity = strtol(merge_verbosity, NULL, 10);
        if (o->verbosity >= 5)
                o->buffer_output = 0;
        strbuf_init(&o->obuf, 0);
@@@ -2252,8 -2252,6 +2253,8 @@@ int parse_merge_opt(struct merge_option
                DIFF_XDL_SET(o, IGNORE_WHITESPACE);
        else if (!strcmp(s, "ignore-space-at-eol"))
                DIFF_XDL_SET(o, IGNORE_WHITESPACE_AT_EOL);
 +      else if (!strcmp(s, "ignore-cr-at-eol"))
 +              DIFF_XDL_SET(o, IGNORE_CR_AT_EOL);
        else if (!strcmp(s, "renormalize"))
                o->renormalize = 1;
        else if (!strcmp(s, "no-renormalize"))