1 files changed, 35 insertions, 16 deletions

diff --git a/merge-recursive.c b/merge-recursive.c
index 113c1d6962..bd053c70df 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -9,6 +9,7 @@
 #include "lockfile.h"
 #include "cache-tree.h"
 #include "object-store.h"
+#include "repository.h"
 #include "commit.h"
 #include "blob.h"
 #include "builtin.h"
@@ -157,7 +158,7 @@ static struct tree *shift_tree_object(struct tree *one, struct tree *two,
 	}
 	if (!oidcmp(&two->object.oid, &shifted))
 		return two;
-	return lookup_tree(&shifted);
+	return lookup_tree(the_repository, &shifted);
 }
 
 static struct commit *make_virtual_commit(struct tree *tree, const char *comment)
@@ -319,7 +320,7 @@ static int add_cacheinfo(struct merge_options *o,
 	struct cache_entry *ce;
 	int ret;
 
-	ce = make_cache_entry(mode, oid ? oid->hash : null_sha1, path, stage, 0);
+	ce = make_cache_entry(&the_index, mode, oid ? oid : &null_oid, path, stage, 0);
 	if (!ce)
 		return err(o, _("add_cacheinfo failed for path '%s'; merge aborting."), path);
 
@@ -327,7 +328,7 @@ static int add_cacheinfo(struct merge_options *o,
 	if (refresh) {
 		struct cache_entry *nce;
 
-		nce = refresh_cache_entry(ce, CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
+		nce = refresh_cache_entry(&the_index, ce, CE_MATCH_REFRESH | CE_MATCH_IGNORE_MISSING);
 		if (!nce)
 			return err(o, _("add_cacheinfo failed to refresh for path '%s'; merge aborting."), path);
 		if (nce != ce)
@@ -415,7 +416,7 @@ struct tree *write_tree_from_memory(struct merge_options *o)
 		return NULL;
 	}
 
-	result = lookup_tree(&active_cache_tree->oid);
+	result = lookup_tree(the_repository, &active_cache_tree->oid);
 
 	return result;
 }
@@ -1191,9 +1192,9 @@ static int merge_submodule(struct merge_options *o,
 		return 0;
 	}
 
-	if (!(commit_base = lookup_commit_reference(base)) ||
-	    !(commit_a = lookup_commit_reference(a)) ||
-	    !(commit_b = lookup_commit_reference(b))) {
+	if (!(commit_base = lookup_commit_reference(the_repository, base)) ||
+	    !(commit_a = lookup_commit_reference(the_repository, a)) ||
+	    !(commit_b = lookup_commit_reference(the_repository, b))) {
 		output(o, 1, _("Failed to merge submodule %s (commits not present)"), path);
 		return 0;
 	}
@@ -3069,10 +3070,26 @@ static int merge_content(struct merge_options *o,
 	if (mfi.clean &&
 	    was_tracked_and_matches(o, path, &mfi.oid, mfi.mode) &&
 	    !df_conflict_remains) {
+		int pos;
+		struct cache_entry *ce;
+
 		output(o, 3, _("Skipped %s (merged same as existing)"), path);
 		if (add_cacheinfo(o, mfi.mode, &mfi.oid, path,
 				  0, (!o->call_depth && !is_dirty), 0))
 			return -1;
+		/*
+		 * However, add_cacheinfo() will delete the old cache entry
+		 * and add a new one.  We need to copy over any skip_worktree
+		 * flag to avoid making the file appear as if it were
+		 * deleted by the user.
+		 */
+		pos = index_name_pos(&o->orig_index, path, strlen(path));
+		ce = o->orig_index.cache[pos];
+		if (ce_skip_worktree(ce)) {
+			pos = index_name_pos(&the_index, path, strlen(path));
+			ce = the_index.cache[pos];
+			ce->ce_flags |= CE_SKIP_WORKTREE;
+		}
 		return mfi.clean;
 	}
 
@@ -3280,6 +3297,13 @@ int merge_trees(struct merge_options *o,
 		struct tree **result)
 {
 	int code, clean;
+	struct strbuf sb = STRBUF_INIT;
+
+	if (!o->call_depth && index_has_changes(&the_index, head, &sb)) {
+		err(o, _("Your local changes to the following files would be overwritten by merge:\n  %s"),
+		    sb.buf);
+		return -1;
+	}
 
 	if (o->subtree_shift) {
 		merge = shift_tree_object(head, merge, o->subtree_shift);
@@ -3287,13 +3311,6 @@ int merge_trees(struct merge_options *o,
 	}
 
 	if (oid_eq(&common->object.oid, &merge->object.oid)) {
-		struct strbuf sb = STRBUF_INIT;
-
-		if (!o->call_depth && 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;
@@ -3426,7 +3443,7 @@ int merge_recursive(struct merge_options *o,
 		/* if there is no common ancestor, use an empty tree */
 		struct tree *tree;
 
-		tree = lookup_tree(the_hash_algo->empty_tree);
+		tree = lookup_tree(the_repository, the_repository->hash_algo->empty_tree);
 		merged_common_ancestors = make_virtual_commit(tree, "ancestor");
 	}
 
@@ -3488,7 +3505,9 @@ static struct commit *get_ref(const struct object_id *oid, const char *name)
 {
 	struct object *object;
 
-	object = deref_tag(parse_object(oid), name, strlen(name));
+	object = deref_tag(the_repository, parse_object(the_repository, oid),
+			   name,
+			   strlen(name));
 	if (!object)
 		return NULL;
 	if (object->type == OBJ_TREE)