Merge pull request #3139 from ethomson/diff_conflicts

Include conflicts when diffing

28 files changed, 675 insertions, 177 deletions

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19463420e..99e375902 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,13 @@ support for HTTPS connections insead of OpenSSL.
   the error message, which allows you to get the "repository not
   found" messages.
 
+* `git_index_conflict_add()` will remove staged entries that exist for
+  conflicted paths.
+
+* The flags for a `git_diff_file` will now have the `GIT_DIFF_FLAG_EXISTS`
+  bit set when a file exists on that side of the diff.  This is useful
+  for understanding whether a side of the diff exists in the presence of
+  a conflict.
 
 ### API additions
 
@@ -98,6 +105,18 @@ support for HTTPS connections insead of OpenSSL.
   configuration of the server, and tools can use this to show messages
   about failing to communicate with the server.
 
+* `git_diff_index_to_workdir()` and `git_diff_tree_to_index()` will now
+  produce deltas of type `GIT_DELTA_CONFLICTED` to indicate that the index
+  side of the delta is a conflict.
+
+* The `git_status` family of functions will now produce status of type
+  `GIT_STATUS_CONFLICTED` to indicate that a conflict exists for that file
+  in the index.
+
+* `git_index_entry_is_conflict()` is a utility function to determine if
+  a given index entry has a non-zero stage entry, indicating that it is
+  one side of a conflict.
+
 ### API removals
 
 * `git_remote_save()` and `git_remote_clear_refspecs()` have been
diff --git a/include/git2/diff.h b/include/git2/diff.h
index cac3b268a..c0d42e30e 100644
--- a/include/git2/diff.h
+++ b/include/git2/diff.h
@@ -226,6 +226,7 @@ typedef enum {
 	GIT_DIFF_FLAG_BINARY     = (1u << 0), /**< file(s) treated as binary data */
 	GIT_DIFF_FLAG_NOT_BINARY = (1u << 1), /**< file(s) treated as text data */
 	GIT_DIFF_FLAG_VALID_ID   = (1u << 2), /**< `id` value is known correct */
+	GIT_DIFF_FLAG_EXISTS     = (1u << 3), /**< file exists at this side of the delta */
 } git_diff_flag_t;
 
 /**
@@ -239,16 +240,17 @@ typedef enum {
  * DELETED pairs).
  */
 typedef enum {
-	GIT_DELTA_UNMODIFIED = 0, /**< no changes */
-	GIT_DELTA_ADDED = 1,	  /**< entry does not exist in old version */
-	GIT_DELTA_DELETED = 2,	  /**< entry does not exist in new version */
-	GIT_DELTA_MODIFIED = 3,   /**< entry content changed between old and new */
-	GIT_DELTA_RENAMED = 4,    /**< entry was renamed between old and new */
-	GIT_DELTA_COPIED = 5,     /**< entry was copied from another old entry */
-	GIT_DELTA_IGNORED = 6,    /**< entry is ignored item in workdir */
-	GIT_DELTA_UNTRACKED = 7,  /**< entry is untracked item in workdir */
-	GIT_DELTA_TYPECHANGE = 8, /**< type of entry changed between old and new */
-	GIT_DELTA_UNREADABLE = 9, /**< entry is unreadable */
+	GIT_DELTA_UNMODIFIED = 0,  /**< no changes */
+	GIT_DELTA_ADDED = 1,	   /**< entry does not exist in old version */
+	GIT_DELTA_DELETED = 2,	   /**< entry does not exist in new version */
+	GIT_DELTA_MODIFIED = 3,    /**< entry content changed between old and new */
+	GIT_DELTA_RENAMED = 4,     /**< entry was renamed between old and new */
+	GIT_DELTA_COPIED = 5,      /**< entry was copied from another old entry */
+	GIT_DELTA_IGNORED = 6,     /**< entry is ignored item in workdir */
+	GIT_DELTA_UNTRACKED = 7,   /**< entry is untracked item in workdir */
+	GIT_DELTA_TYPECHANGE = 8,  /**< type of entry changed between old and new */
+	GIT_DELTA_UNREADABLE = 9,  /**< entry is unreadable */
+	GIT_DELTA_CONFLICTED = 10, /**< entry in the index is conflicted */
 } git_delta_t;
 
 /**
diff --git a/include/git2/index.h b/include/git2/index.h
index 52032f7fd..49bbe1614 100644
--- a/include/git2/index.h
+++ b/include/git2/index.h
@@ -430,6 +430,15 @@ GIT_EXTERN(int) git_index_add(git_index *index, const git_index_entry *source_en
  */
 GIT_EXTERN(int) git_index_entry_stage(const git_index_entry *entry);
 
+/**
+ * Return whether the given index entry is a conflict (has a high stage
+ * entry).  This is simply shorthand for `git_index_entry_stage > 0`.
+ *
+ * @param entry The entry
+ * @return 1 if the entry is a conflict entry, 0 otherwise
+ */
+GIT_EXTERN(int) git_index_entry_is_conflict(const git_index_entry *entry);
+
 /**@}*/
 
 /** @name Workdir Index Entry Functions
@@ -631,7 +640,8 @@ GIT_EXTERN(int) git_index_find(size_t *at_pos, git_index *index, const char *pat
 /**@{*/
 
 /**
- * Add or update index entries to represent a conflict
+ * Add or update index entries to represent a conflict.  Any staged
+ * entries that exist at the given paths will be removed.
  *
  * The entries are the entries from the tree included in the merge.  Any
  * entry may be null to indicate that that file was not present in the
diff --git a/include/git2/status.h b/include/git2/status.h
index 5f211810d..671113955 100644
--- a/include/git2/status.h
+++ b/include/git2/status.h
@@ -46,6 +46,7 @@ typedef enum {
 	GIT_STATUS_WT_UNREADABLE    = (1u << 12),
 
 	GIT_STATUS_IGNORED          = (1u << 14),
+	GIT_STATUS_CONFLICTED       = (1u << 15),
 } git_status_t;
 
 /**
diff --git a/src/diff.c b/src/diff.c
index f7e1c8ee4..c9d1d8730 100644
--- a/src/diff.c
+++ b/src/diff.c
@@ -77,11 +77,24 @@ static int diff_insert_delta(
 static int diff_delta__from_one(
 	git_diff *diff,
 	git_delta_t status,
-	const git_index_entry *entry)
+	const git_index_entry *oitem,
+	const git_index_entry *nitem)
 {
+	const git_index_entry *entry = nitem;
+	bool has_old = false;
 	git_diff_delta *delta;
 	const char *matched_pathspec;
 
+	assert((oitem != NULL) ^ (nitem != NULL));
+
+	if (oitem) {
+		entry = oitem;
+		has_old = true;
+	}
+
+	if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_REVERSE))
+		has_old = !has_old;
+
 	if ((entry->flags & GIT_IDXENTRY_VALID) != 0)
 		return 0;
 
@@ -111,20 +124,21 @@ static int diff_delta__from_one(
 	assert(status != GIT_DELTA_MODIFIED);
 	delta->nfiles = 1;
 
-	if (delta->status == GIT_DELTA_DELETED) {
+	if (has_old) {
 		delta->old_file.mode = entry->mode;
 		delta->old_file.size = entry->file_size;
+		delta->old_file.flags |= GIT_DIFF_FLAG_EXISTS;
 		git_oid_cpy(&delta->old_file.id, &entry->id);
 	} else /* ADDED, IGNORED, UNTRACKED */ {
 		delta->new_file.mode = entry->mode;
 		delta->new_file.size = entry->file_size;
+		delta->new_file.flags |= GIT_DIFF_FLAG_EXISTS;
 		git_oid_cpy(&delta->new_file.id, &entry->id);
 	}
 
 	delta->old_file.flags |= GIT_DIFF_FLAG_VALID_ID;
 
-	if (delta->status == GIT_DELTA_DELETED ||
-		!git_oid_iszero(&delta->new_file.id))
+	if (has_old || !git_oid_iszero(&delta->new_file.id))
 		delta->new_file.flags |= GIT_DIFF_FLAG_VALID_ID;
 
 	return diff_insert_delta(diff, delta, matched_pathspec);
@@ -137,9 +151,10 @@ static int diff_delta__from_two(
 	uint32_t old_mode,
 	const git_index_entry *new_entry,
 	uint32_t new_mode,
-	git_oid *new_oid,
+	const git_oid *new_id,
 	const char *matched_pathspec)
 {
+	const git_oid *old_id = &old_entry->id;
 	git_diff_delta *delta;
 	const char *canonical_path = old_entry->path;
 
@@ -147,38 +162,45 @@ static int diff_delta__from_two(
 		DIFF_FLAG_ISNT_SET(diff, GIT_DIFF_INCLUDE_UNMODIFIED))
 		return 0;
 
+	if (!new_id)
+		new_id = &new_entry->id;
+
 	if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_REVERSE)) {
 		uint32_t temp_mode = old_mode;
 		const git_index_entry *temp_entry = old_entry;
+		const git_oid *temp_id = old_id;
+
 		old_entry = new_entry;
 		new_entry = temp_entry;
 		old_mode = new_mode;
 		new_mode = temp_mode;
+		old_id = new_id;
+		new_id = temp_id;
 	}
 
 	delta = diff_delta__alloc(diff, status, canonical_path);
 	GITERR_CHECK_ALLOC(delta);
 	delta->nfiles = 2;
 
-	git_oid_cpy(&delta->old_file.id, &old_entry->id);
-	delta->old_file.size = old_entry->file_size;
-	delta->old_file.mode = old_mode;
-	delta->old_file.flags |= GIT_DIFF_FLAG_VALID_ID;
+	if (!git_index_entry_is_conflict(old_entry)) {
+		delta->old_file.size = old_entry->file_size;
+		delta->old_file.mode = old_mode;
+		git_oid_cpy(&delta->old_file.id, old_id);
+		delta->old_file.flags |= GIT_DIFF_FLAG_VALID_ID |
+			GIT_DIFF_FLAG_EXISTS;
+	}
 
-	git_oid_cpy(&delta->new_file.id, &new_entry->id);
-	delta->new_file.size = new_entry->file_size;
-	delta->new_file.mode = new_mode;
+	if (!git_index_entry_is_conflict(new_entry)) {
+		git_oid_cpy(&delta->new_file.id, new_id);
+		delta->new_file.size = new_entry->file_size;
+		delta->new_file.mode = new_mode;
+		delta->old_file.flags |= GIT_DIFF_FLAG_EXISTS;
+		delta->new_file.flags |= GIT_DIFF_FLAG_EXISTS;
 
-	if (new_oid) {
-		if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_REVERSE))
-			git_oid_cpy(&delta->old_file.id, new_oid);
-		else
-			git_oid_cpy(&delta->new_file.id, new_oid);
+		if (!git_oid_iszero(&new_entry->id))
+			delta->new_file.flags |= GIT_DIFF_FLAG_VALID_ID;
 	}
 
-	if (new_oid || !git_oid_iszero(&new_entry->id))
-		delta->new_file.flags |= GIT_DIFF_FLAG_VALID_ID;
-
 	return diff_insert_delta(diff, delta, matched_pathspec);
 }
 
@@ -327,6 +349,22 @@ static const char *diff_mnemonic_prefix(
 	return pfx;
 }
 
+static int diff_entry_cmp(const void *a, const void *b)
+{
+	const git_index_entry *entry_a = a;
+	const git_index_entry *entry_b = b;
+
+	return strcmp(entry_a->path, entry_b->path);
+}
+
+static int diff_entry_icmp(const void *a, const void *b)
+{
+	const git_index_entry *entry_a = a;
+	const git_index_entry *entry_b = b;
+
+	return strcasecmp(entry_a->path, entry_b->path);
+}
+
 static void diff_set_ignore_case(git_diff *diff, bool ignore_case)
 {
 	if (!ignore_case) {
@@ -335,7 +373,7 @@ static void diff_set_ignore_case(git_diff *diff, bool ignore_case)
 		diff->strcomp    = git__strcmp;
 		diff->strncomp   = git__strncmp;
 		diff->pfxcomp    = git__prefixcmp;
-		diff->entrycomp  = git_index_entry_cmp;
+		diff->entrycomp  = diff_entry_cmp;
 
 		git_vector_set_cmp(&diff->deltas, git_diff_delta__cmp);
 	} else {
@@ -344,7 +382,7 @@ static void diff_set_ignore_case(git_diff *diff, bool ignore_case)
 		diff->strcomp    = git__strcasecmp;
 		diff->strncomp   = git__strncasecmp;
 		diff->pfxcomp    = git__prefixcmp_icase;
-		diff->entrycomp  = git_index_entry_icmp;
+		diff->entrycomp  = diff_entry_icmp;
 
 		git_vector_set_cmp(&diff->deltas, git_diff_delta__casecmp);
 	}
@@ -731,40 +769,47 @@ static int maybe_modified(
 		new_is_workdir)
 		nmode = (nmode & ~MODE_BITS_MASK) | (omode & MODE_BITS_MASK);
 
+	/* if one side is a conflict, mark the whole delta as conflicted */
+	if (git_index_entry_is_conflict(oitem) ||
+			git_index_entry_is_conflict(nitem)) {
+		status = GIT_DELTA_CONFLICTED;
+
 	/* support "assume unchanged" (poorly, b/c we still stat everything) */
-	if ((oitem->flags & GIT_IDXENTRY_VALID) != 0)
+	} else if ((oitem->flags & GIT_IDXENTRY_VALID) != 0) {
 		status = GIT_DELTA_UNMODIFIED;
 
 	/* support "skip worktree" index bit */
-	else if ((oitem->flags_extended & GIT_IDXENTRY_SKIP_WORKTREE) != 0)
+	} else if ((oitem->flags_extended & GIT_IDXENTRY_SKIP_WORKTREE) != 0) {
 		status = GIT_DELTA_UNMODIFIED;
 
 	/* if basic type of file changed, then split into delete and add */
-	else if (GIT_MODE_TYPE(omode) != GIT_MODE_TYPE(nmode)) {
-		if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_INCLUDE_TYPECHANGE))
+	} else if (GIT_MODE_TYPE(omode) != GIT_MODE_TYPE(nmode)) {
+		if (DIFF_FLAG_IS_SET(diff, GIT_DIFF_INCLUDE_TYPECHANGE)) {
 			status = GIT_DELTA_TYPECHANGE;
+		}
+
 		else if (nmode == GIT_FILEMODE_UNREADABLE) {
-			if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem)))
-				error = diff_delta__from_one(diff, GIT_DELTA_UNREADABLE, nitem);
+			if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem, NULL)))
+				error = diff_delta__from_one(diff, GIT_DELTA_UNREADABLE, NULL, nitem);
 			return error;
 		}
+
 		else {
-			if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem)))
-				error = diff_delta__from_one(diff, GIT_DELTA_ADDED, nitem);
+			if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem, NULL)))
+				error = diff_delta__from_one(diff, GIT_DELTA_ADDED, NULL, nitem);
 			return error;
 		}
-	}
 
 	/* if oids and modes match (and are valid), then file is unmodified */
-	else if (git_oid_equal(&oitem->id, &nitem->id) &&
+	} else if (git_oid_equal(&oitem->id, &nitem->id) &&
 			 omode == nmode &&
-			 !git_oid_iszero(&oitem->id))
+			 !git_oid_iszero(&oitem->id)) {
 		status = GIT_DELTA_UNMODIFIED;
 
 	/* if we have an unknown OID and a workdir iterator, then check some
 	 * circumstances that can accelerate things or need special handling
 	 */
-	else if (git_oid_iszero(&nitem->id) && new_is_workdir) {
+	} else if (git_oid_iszero(&nitem->id) && new_is_workdir) {
 		bool use_ctime = ((diff->diffcaps & GIT_DIFFCAPS_TRUST_CTIME) != 0);
 		bool use_nanos = ((diff->diffcaps & GIT_DIFFCAPS_TRUST_NANOSECS) != 0);
 
@@ -795,12 +840,12 @@ static int maybe_modified(
 			status = GIT_DELTA_MODIFIED;
 			modified_uncertain = true;
 		}
-	}
 
 	/* if mode is GITLINK and submodules are ignored, then skip */
-	else if (S_ISGITLINK(nmode) &&
-			 DIFF_FLAG_IS_SET(diff, GIT_DIFF_IGNORE_SUBMODULES))
+	} else if (S_ISGITLINK(nmode) &&
+			 DIFF_FLAG_IS_SET(diff, GIT_DIFF_IGNORE_SUBMODULES)) {
 		status = GIT_DELTA_UNMODIFIED;
+	}
 
 	/* if we got here and decided that the files are modified, but we
 	 * haven't calculated the OID of the new item, then calculate it now
@@ -809,6 +854,7 @@ static int maybe_modified(
 		const git_oid *update_check =
 			DIFF_FLAG_IS_SET(diff, GIT_DIFF_UPDATE_INDEX) && omode == nmode ?
 			&oitem->id : NULL;
+
 		if ((error = git_diff__oid_for_entry(
 				&noid, diff, nitem, update_check)) < 0)
 			return error;
@@ -830,8 +876,9 @@ static int maybe_modified(
 		DIFF_FLAG_IS_SET(diff, GIT_DIFF_INCLUDE_CASECHANGE) &&
 		strcmp(oitem->path, nitem->path) != 0) {
 
-		if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem)))
-			error = diff_delta__from_one(diff, GIT_DELTA_ADDED, nitem);
+		if (!(error = diff_delta__from_one(diff, GIT_DELTA_DELETED, oitem, NULL)))
+			error = diff_delta__from_one(diff, GIT_DELTA_ADDED, NULL, nitem);
+
 		return error;
 	}
 
@@ -857,6 +904,84 @@ static bool entry_is_prefixed(
 			item->path[pathlen] == '/');
 }
 
+static int iterator_current(
+	const git_index_entry **entry,
+	git_iterator *iterator)
+{
+	int error;
+
+	if ((error = git_iterator_current(entry, iterator)) == GIT_ITEROVER) {
+		*entry = NULL;
+		error = 0;
+	}
+
+	return error;
+}
+
+static int iterator_advance(
+	const git_index_entry **entry,
+	git_iterator *iterator)
+{
+	const git_index_entry *prev_entry = *entry;
+	int cmp, error;
+
+	/* if we're looking for conflicts, we only want to report
+	 * one conflict for each file, instead of all three sides.
+	 * so if this entry is a conflict for this file, and the
+	 * previous one was a conflict for the same file, skip it.
+	 */
+	while ((error = git_iterator_advance(entry, iterator)) == 0) {
+		if (!(iterator->flags & GIT_ITERATOR_INCLUDE_CONFLICTS) ||
+			!git_index_entry_is_conflict(prev_entry) ||
+			!git_index_entry_is_conflict(*entry))
+			break;
+
+		cmp = (iterator->flags & GIT_ITERATOR_IGNORE_CASE) ?
+			strcasecmp(prev_entry->path, (*entry)->path) :
+			strcmp(prev_entry->path, (*entry)->path);
+
+		if (cmp)
+			break;
+	}
+
+	if (error == GIT_ITEROVER) {
+		*entry = NULL;
+		error = 0;
+	}
+
+	return error;
+}
+
+static int iterator_advance_into(
+	const git_index_entry **entry,
+	git_iterator *iterator)
+{
+	int error;
+
+	if ((error = git_iterator_advance_into(entry, iterator)) == GIT_ITEROVER) {
+		*entry = NULL;
+		error = 0;
+	}
+
+	return error;
+}
+
+static int iterator_advance_over_with_status(
+	const git_index_entry **entry,
+	git_iterator_status_t *status,
+	git_iterator *iterator)
+{
+	int error;
+
+	if ((error = git_iterator_advance_over_with_status(
+			entry, status, iterator)) == GIT_ITEROVER) {
+		*entry = NULL;
+		error = 0;
+	}
+
+	return error;
+}
+
 static int handle_unmatched_new_item(
 	git_diff *diff, diff_in_progress *info)
 {
@@ -868,8 +993,12 @@ static int handle_unmatched_new_item(
 	/* check if this is a prefix of the other side */
 	contains_oitem = entry_is_prefixed(diff, info->oitem, nitem);
 
+	/* update delta_type if this item is conflicted */
+	if (git_index_entry_is_conflict(nitem))
+		delta_type = GIT_DELTA_CONFLICTED;
+
 	/* update delta_type if this item is ignored */
-	if (git_iterator_current_is_ignored(info->new_iter))
+	else if (git_iterator_current_is_ignored(info->new_iter))
 		delta_type = GIT_DELTA_IGNORED;
 
 	if (nitem->mode == GIT_FILEMODE_TREE) {
@@ -904,18 +1033,17 @@ static int handle_unmatched_new_item(
 			git_iterator_status_t untracked_state;
 
 			/* attempt to insert record for this directory */
-			if ((error = diff_delta__from_one(diff, delta_type, nitem)) != 0)
+			if ((error = diff_delta__from_one(diff, delta_type, NULL, nitem)) != 0)
 				return error;
 
 			/* if delta wasn't created (because of rules), just skip ahead */
 			last = diff_delta__last_for_item(diff, nitem);
 			if (!last)
-				return git_iterator_advance(&info->nitem, info->new_iter);
+				return iterator_advance(&info->nitem, info->new_iter);
 
 			/* iterate into dir looking for an actual untracked file */
-			if ((error = git_iterator_advance_over_with_status(
-					&info->nitem, &untracked_state, info->new_iter)) < 0 &&
-				error != GIT_ITEROVER)
+			if ((error = iterator_advance_over_with_status(
+					&info->nitem, &untracked_state, info->new_iter)) < 0)
 				return error;
 
 			/* if we found nothing or just ignored items, update the record */
@@ -935,7 +1063,7 @@ static int handle_unmatched_new_item(
 
 		/* try to advance into directory if necessary */
 		if (recurse_into_dir) {
-			error = git_iterator_advance_into(&info->nitem, info->new_iter);
+			error = iterator_advance_into(&info->nitem, info->new_iter);
 
 			/* if real error or no error, proceed with iteration */
 			if (error != GIT_ENOTFOUND)
@@ -946,7 +1074,7 @@ static int handle_unmatched_new_item(
 			 * it or ignore it
 			 */
 			if (contains_oitem)
-				return git_iterator_advance(&info->nitem, info->new_iter);
+				return iterator_advance(&info->nitem, info->new_iter);
 			delta_type = GIT_DELTA_IGNORED;
 		}
 	}
@@ -955,7 +1083,7 @@ static int handle_unmatched_new_item(
 		DIFF_FLAG_ISNT_SET(diff, GIT_DIFF_RECURSE_IGNORED_DIRS) &&
 		git_iterator_current_tree_is_ignored(info->new_iter))
 		/* item contained in ignored directory, so skip over it */
-		return git_iterator_advance(&info->nitem, info->new_iter);
+		return iterator_advance(&info->nitem, info->new_iter);
 
 	else if (info->new_iter->type != GIT_ITERATOR_TYPE_WORKDIR)
 		delta_type = GIT_DELTA_ADDED;
@@ -968,12 +1096,12 @@ static int handle_unmatched_new_item(
 
 			/* if this contains a tracked item, treat as normal TREE */
 			if (contains_oitem) {
-				error = git_iterator_advance_into(&info->nitem, info->new_iter);
+				error = iterator_advance_into(&info->nitem, info->new_iter);
 				if (error != GIT_ENOTFOUND)
 					return error;
 
 				giterr_clear();
-				return git_iterator_advance(&info->nitem, info->new_iter);
+				return iterator_advance(&info->nitem, info->new_iter);
 			}
 		}
 	}
@@ -986,7 +1114,7 @@ static int handle_unmatched_new_item(
 	}
 
 	/* Actually create the record for this item if necessary */
-	if ((error = diff_delta__from_one(diff, delta_type, nitem)) != 0)
+	if ((error = diff_delta__from_one(diff, delta_type, NULL, nitem)) != 0)
 		return error;
 
 	/* If user requested TYPECHANGE records, then check for that instead of
@@ -1004,14 +1132,20 @@ static int handle_unmatched_new_item(
 		}
 	}
 
-	return git_iterator_advance(&info->nitem, info->new_iter);
+	return iterator_advance(&info->nitem, info->new_iter);
 }
 
 static int handle_unmatched_old_item(
 	git_diff *diff, diff_in_progress *info)
 {
-	int error = diff_delta__from_one(diff, GIT_DELTA_DELETED, info->oitem);
-	if (error != 0)
+	git_delta_t delta_type = GIT_DELTA_DELETED;
+	int error;
+
+	/* update delta_type if this item is conflicted */
+	if (git_index_entry_is_conflict(info->oitem))
+		delta_type = GIT_DELTA_CONFLICTED;
+
+	if ((error = diff_delta__from_one(diff, delta_type, info->oitem, NULL)) < 0)
 		return error;
 
 	/* if we are generating TYPECHANGE records then check for that
@@ -1033,10 +1167,10 @@ static int handle_unmatched_old_item(
 		 */
 		if (S_ISDIR(info->nitem->mode) &&
 			DIFF_FLAG_ISNT_SET(diff, GIT_DIFF_RECURSE_UNTRACKED_DIRS))
-			return git_iterator_advance(&info->nitem, info->new_iter);
+			return iterator_advance(&info->nitem, info->new_iter);
 	}
 
-	return git_iterator_advance(&info->oitem, info->old_iter);
+	return iterator_advance(&info->oitem, info->old_iter);
 }
 
 static int handle_matched_item(
@@ -1047,9 +1181,8 @@ static int handle_matched_item(
 	if ((error = maybe_modified(diff, info)) < 0)
 		return error;
 
-	if (!(error = git_iterator_advance(&info->oitem, info->old_iter)) ||
-		error == GIT_ITEROVER)
-		error = git_iterator_advance(&info->nitem, info->new_iter);
+	if (!(error = iterator_advance(&info->oitem, info->old_iter)))
+		error = iterator_advance(&info->nitem, info->new_iter);
 
 	return error;
 }
@@ -1085,13 +1218,9 @@ int git_diff__from_iterators(
 	if ((error = diff_list_apply_options(diff, opts)) < 0)
 		goto cleanup;
 
-	if ((error = git_iterator_current(&info.oitem, old_iter)) < 0 &&
-		error != GIT_ITEROVER)
+	if ((error = iterator_current(&info.oitem, old_iter)) < 0 ||
+		(error = iterator_current(&info.nitem, new_iter)) < 0)
 		goto cleanup;
-	if ((error = git_iterator_current(&info.nitem, new_iter)) < 0 &&
-		error != GIT_ITEROVER)
-		goto cleanup;
-	error = 0;
 
 	/* run iterators building diffs */
 	while (!error && (info.oitem || info.nitem)) {
@@ -1113,10 +1242,6 @@ int git_diff__from_iterators(
 		 */
 		else
 			error = handle_matched_item(diff, &info);
-
-		/* because we are iterating over two lists, ignore ITEROVER */
-		if (error == GIT_ITEROVER)
-			error = 0;
 	}
 
 	diff->perf.stat_calls += old_iter->stat_calls + new_iter->stat_calls;
@@ -1186,6 +1311,8 @@ int git_diff_tree_to_index(
 {
 	int error = 0;
 	bool index_ignore_case = false;
+	git_iterator_flag_t iflag = GIT_ITERATOR_DONT_IGNORE_CASE |
+		GIT_ITERATOR_INCLUDE_CONFLICTS;
 
 	assert(diff && repo);
 
@@ -1195,10 +1322,8 @@ int git_diff_tree_to_index(
 	index_ignore_case = index->ignore_case;
 
 	DIFF_FROM_ITERATORS(
-		git_iterator_for_tree(
-			&a, old_tree, GIT_ITERATOR_DONT_IGNORE_CASE, pfx, pfx),
-		git_iterator_for_index(
-			&b, index, GIT_ITERATOR_DONT_IGNORE_CASE, pfx, pfx)
+		git_iterator_for_tree(&a, old_tree, iflag, pfx, pfx),
+		git_iterator_for_index(&b, index, iflag, pfx, pfx)
 	);
 
 	/* if index is in case-insensitive order, re-sort deltas to match */
@@ -1222,7 +1347,8 @@ int git_diff_index_to_workdir(
 		return error;
 
 	DIFF_FROM_ITERATORS(
-		git_iterator_for_index(&a, index, 0, pfx, pfx),
+		git_iterator_for_index(
+			&a, index, GIT_ITERATOR_INCLUDE_CONFLICTS, pfx, pfx),
 		git_iterator_for_workdir(
 			&b, repo, index, NULL, GIT_ITERATOR_DONT_AUTOEXPAND, pfx, pfx)
 	);
diff --git a/src/index.c b/src/index.c
index 561fe73c4..0422ff1d4 100644
--- a/src/index.c
+++ b/src/index.c
@@ -1173,6 +1173,9 @@ int git_index_remove_bypath(git_index *index, const char *path)
 		ret != GIT_ENOTFOUND))
 		return ret;
 
+	if (ret == GIT_ENOTFOUND)
+		giterr_clear();
+
 	return 0;
 }
 
@@ -1314,6 +1317,30 @@ int git_index_conflict_add(git_index *index,
 		(ret = index_entry_dup(&entries[2], INDEX_OWNER(index), their_entry)) < 0)
 		goto on_error;
 
+	/* Validate entries */
+	for (i = 0; i < 3; i++) {
+		if (entries[i] && !valid_filemode(entries[i]->mode)) {
+			giterr_set(GITERR_INDEX, "invalid filemode for stage %d entry",
+				i);
+			return -1;
+		}
+	}
+
+	/* Remove existing index entries for each path */
+	for (i = 0; i < 3; i++) {
+		if (entries[i] == NULL)
+			continue;
+
+		if ((ret = git_index_remove(index, entries[i]->path, 0)) != 0) {
+			if (ret != GIT_ENOTFOUND)
+				goto on_error;
+
+			giterr_clear();
+			ret = 0;
+		}
+	}
+
+	/* Add the conflict entries */
 	for (i = 0; i < 3; i++) {
 		if (entries[i] == NULL)
 			continue;
@@ -1321,7 +1348,7 @@ int git_index_conflict_add(git_index *index,
 		/* Make sure stage is correct */
 		GIT_IDXENTRY_STAGE_SET(entries[i], i + 1);
 
-		if ((ret = index_insert(index, &entries[i], 1, true)) < 0)
+		if ((ret = index_insert(index, &entries[i], 0, true)) < 0)
 			goto on_error;
 
 		entries[i] = NULL; /* don't free if later entry fails */
@@ -1510,7 +1537,7 @@ int git_index_conflict_next(
 	while (iterator->cur < iterator->index->entries.length) {
 		entry = git_index_get_byindex(iterator->index, iterator->cur);
 
-		if (git_index_entry_stage(entry) > 0) {
+		if (git_index_entry_is_conflict(entry)) {
 			if ((len = index_conflict__get_byindex(
 				ancestor_out,
 				our_out,
@@ -2356,6 +2383,11 @@ int git_index_entry_stage(const git_index_entry *entry)
 	return GIT_IDXENTRY_STAGE(entry);
 }
 
+int git_index_entry_is_conflict(const git_index_entry *entry)
+{
+	return (GIT_IDXENTRY_STAGE(entry) > 0);
+}
+
 typedef struct read_tree_data {
 	git_index *index;
 	git_vector *old_entries;
@@ -2638,7 +2670,8 @@ static int apply_each_file(const git_diff_delta *delta, float progress, void *pa
 	if (error < 0) /* actual error */
 		return error;
 
-	if (delta->status == GIT_DELTA_DELETED)
+	/* If the workdir item does not exist, remove it from the index. */
+	if ((delta->new_file.flags & GIT_DIFF_FLAG_EXISTS) == 0)
 		error = git_index_remove_bypath(data->index, path);
 	else
 		error = git_index_add_bypath(data->index, delta->new_file.path);
diff --git a/src/iterator.c b/src/iterator.c
index c5c5fd7ce..93303a87d 100644
--- a/src/iterator.c
+++ b/src/iterator.c
@@ -46,6 +46,7 @@
 #define iterator__include_trees(I)   iterator__flag(I,INCLUDE_TREES)
 #define iterator__dont_autoexpand(I) iterator__flag(I,DONT_AUTOEXPAND)
 #define iterator__do_autoexpand(I)   !iterator__flag(I,DONT_AUTOEXPAND)
+#define iterator__include_conflicts(I) iterator__flag(I, INCLUDE_CONFLICTS)
 
 #define GIT_ITERATOR_FIRST_ACCESS (1 << 15)
 #define iterator__has_been_accessed(I) iterator__flag(I,FIRST_ACCESS)
@@ -668,13 +669,16 @@ static const git_index_entry *index_iterator__index_entry(index_iterator *ii)
 	return ie;
 }
 
-static const git_index_entry *index_iterator__skip_conflicts(index_iterator *ii)
+static const git_index_entry *index_iterator__advance_over_conflicts(index_iterator *ii)
 {
-	const git_index_entry *ie;
+	const git_index_entry *ie = index_iterator__index_entry(ii);
 
-	while ((ie = index_iterator__index_entry(ii)) != NULL &&
-		   git_index_entry_stage(ie) != 0)
-		ii->current++;
+	if (!iterator__include_conflicts(ii)) {
+		while (ie && git_index_entry_is_conflict(ie)) {
+			ii->current++;
+			ie = index_iterator__index_entry(ii);
+		}
+	}
 
 	return ie;
 }
@@ -702,7 +706,7 @@ static void index_iterator__next_prefix_tree(index_iterator *ii)
 
 static int index_iterator__first_prefix_tree(index_iterator *ii)
 {
-	const git_index_entry *ie = index_iterator__skip_conflicts(ii);
+	const git_index_entry *ie = index_iterator__advance_over_conflicts(ii);
 	const char *scan, *prior, *slash;
 
 	if (!ie || !iterator__include_trees(ii))
@@ -825,7 +829,7 @@ static int index_iterator__reset(
 		git_index_snapshot_find(
 			&ii->current, &ii->entries, ii->entry_srch, ii->base.start, 0, 0);
 
-	if ((ie = index_iterator__skip_conflicts(ii)) == NULL)
+	if ((ie = index_iterator__advance_over_conflicts(ii)) == NULL)
 		return 0;
 
 	if (git_buf_sets(&ii->partial, ie->path) < 0)
diff --git a/src/iterator.h b/src/iterator.h
index 1520bffc2..db1f325a7 100644
--- a/src/iterator.h
+++ b/src/iterator.h
@@ -33,6 +33,8 @@ typedef enum {
 	GIT_ITERATOR_DONT_AUTOEXPAND  = (1u << 3),
 	/** convert precomposed unicode to decomposed unicode */
 	GIT_ITERATOR_PRECOMPOSE_UNICODE = (1u << 4),
+	/** include conflicts */
+	GIT_ITERATOR_INCLUDE_CONFLICTS = (1u << 5),
 } git_iterator_flag_t;
 
 typedef struct {
diff --git a/src/merge.c b/src/merge.c
index 5e7727429..eaf7eee1f 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -2492,7 +2492,7 @@ int git_merge__check_result(git_repository *repo, git_index *index_new)
 	for (i = 0; i < git_index_entrycount(index_new); i++) {
 		e = git_index_get_byindex(index_new, i);
 
-		if (git_index_entry_stage(e) != 0 &&
+		if (git_index_entry_is_conflict(e) &&
 			(git_vector_last(&paths) == NULL ||
 			strcmp(git_vector_last(&paths), e->path) != 0)) {
 
@@ -2544,7 +2544,7 @@ int git_merge__append_conflicts_to_merge_msg(
 	for (i = 0; i < git_index_entrycount(index); i++) {
 		const git_index_entry *e = git_index_get_byindex(index, i);
 
-		if (git_index_entry_stage(e) == 0)
+		if (!git_index_entry_is_conflict(e))
 			continue;
 
 		if (last == NULL || strcmp(e->path, last) != 0)
diff --git a/src/reset.c b/src/reset.c
index d08e48cd7..0ffa51b66 100644
--- a/src/reset.c
+++ b/src/reset.c
@@ -63,6 +63,7 @@ int git_reset_default(
 
 		assert(delta->status == GIT_DELTA_ADDED ||
 			delta->status == GIT_DELTA_MODIFIED ||
+			delta->status == GIT_DELTA_CONFLICTED ||
 			delta->status == GIT_DELTA_DELETED);
 
 		error = git_index_conflict_remove(index, delta->old_file.path);
diff --git a/src/status.c b/src/status.c
index 720ccb7eb..b206b0e2f 100644
--- a/src/status.c
+++ b/src/status.c
@@ -44,6 +44,9 @@ static unsigned int index_delta2status(const git_diff_delta *head2idx)
 	case GIT_DELTA_TYPECHANGE:
 		st = GIT_STATUS_INDEX_TYPECHANGE;
 		break;
+	case GIT_DELTA_CONFLICTED:
+		st = GIT_STATUS_CONFLICTED;
+		break;
 	default:
 		break;
 	}
@@ -102,6 +105,9 @@ static unsigned int workdir_delta2status(
 	case GIT_DELTA_TYPECHANGE:
 		st = GIT_STATUS_WT_TYPECHANGE;
 		break;
+	case GIT_DELTA_CONFLICTED:
+		st = GIT_STATUS_CONFLICTED;
+		break;
 	default:
 		break;
 	}
diff --git a/tests/checkout/conflict.c b/tests/checkout/conflict.c
index 3d763af12..006dc6522 100644
--- a/tests/checkout/conflict.c
+++ b/tests/checkout/conflict.c
@@ -102,7 +102,7 @@ static void create_index(struct checkout_index_entry *entries, size_t entries_le
 		memset(&entry, 0x0, sizeof(git_index_entry));
 
 		entry.mode = entries[i].mode;
-		entry.flags = entries[i].stage << GIT_IDXENTRY_STAGESHIFT;
+		GIT_IDXENTRY_STAGE_SET(&entry, entries[i].stage);
 		git_oid_fromstr(&entry.id, entries[i].oid_str);
 		entry.path = entries[i].path;
 
diff --git a/tests/checkout/index.c b/tests/checkout/index.c
index de0770dba..89b014586 100644
--- a/tests/checkout/index.c
+++ b/tests/checkout/index.c
@@ -685,15 +685,15 @@ static void add_conflict(git_index *index, const char *path)
 	entry.path = path;
 
 	git_oid_fromstr(&entry.id, "d427e0b2e138501a3d15cc376077a3631e15bd46");
-	entry.flags = (1 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 1);
 	cl_git_pass(git_index_add(index, &entry));
 
 	git_oid_fromstr(&entry.id, "4e886e602529caa9ab11d71f86634bd1b6e0de10");
-	entry.flags = (2 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 2);
 	cl_git_pass(git_index_add(index, &entry));
 
 	git_oid_fromstr(&entry.id, "2bd0a343aeef7a2cf0d158478966a6e587ff3863");
-	entry.flags = (3 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 3);
 	cl_git_pass(git_index_add(index, &entry));
 }
 
diff --git a/tests/checkout/tree.c b/tests/checkout/tree.c
index 50541a703..462323186 100644
--- a/tests/checkout/tree.c
+++ b/tests/checkout/tree.c
@@ -893,16 +893,16 @@ static void create_conflict(const char *path)
 
 	memset(&entry, 0x0, sizeof(git_index_entry));
 	entry.mode = 0100644;
-	entry.flags = 1 << GIT_IDXENTRY_STAGESHIFT;
+	GIT_IDXENTRY_STAGE_SET(&entry, 1);
 	git_oid_fromstr(&entry.id, "d427e0b2e138501a3d15cc376077a3631e15bd46");
 	entry.path = path;
 	cl_git_pass(git_index_add(index, &entry));
 
-	entry.flags = 2 << GIT_IDXENTRY_STAGESHIFT;
+	GIT_IDXENTRY_STAGE_SET(&entry, 2);
 	git_oid_fromstr(&entry.id, "ee3fa1b8c00aff7fe02065fdb50864bb0d932ccf");
 	cl_git_pass(git_index_add(index, &entry));
 
-	entry.flags = 3 << GIT_IDXENTRY_STAGESHIFT;
+	GIT_IDXENTRY_STAGE_SET(&entry, 3);
 	git_oid_fromstr(&entry.id, "2bd0a343aeef7a2cf0d158478966a6e587ff3863");
 	cl_git_pass(git_index_add(index, &entry));
 
diff --git a/tests/clar_libgit2.c b/tests/clar_libgit2.c
index 6087c2a67..dabc47a09 100644
--- a/tests/clar_libgit2.c
+++ b/tests/clar_libgit2.c
@@ -197,6 +197,14 @@ git_repository *cl_git_sandbox_init(const char *sandbox)
 	return _cl_repo;
 }
 
+git_repository *cl_git_sandbox_init_new(const char *sandbox)
+{
+	cl_git_pass(git_repository_init(&_cl_repo, sandbox, false));
+	_cl_sandbox = sandbox;
+
+	return _cl_repo;
+}
+
 git_repository *cl_git_sandbox_reopen(void)
 {
 	if (_cl_repo) {
diff --git a/tests/clar_libgit2.h b/tests/clar_libgit2.h
index 86c90b049..9ab0da4f6 100644
--- a/tests/clar_libgit2.h
+++ b/tests/clar_libgit2.h
@@ -127,6 +127,7 @@ int cl_rename(const char *source, const char *dest);
 /* Git sandbox setup helpers */
 
 git_repository *cl_git_sandbox_init(const char *sandbox);
+git_repository *cl_git_sandbox_init_new(const char *name);
 void cl_git_sandbox_cleanup(void);
 git_repository *cl_git_sandbox_reopen(void);
 
diff --git a/tests/diff/diff_helpers.c b/tests/diff/diff_helpers.c
index 47e06f0d8..03862d6b4 100644
--- a/tests/diff/diff_helpers.c
+++ b/tests/diff/diff_helpers.c
@@ -68,7 +68,7 @@ int diff_file_cb(
 	if ((delta->flags & GIT_DIFF_FLAG_BINARY) != 0)
 		e->files_binary++;
 
-	cl_assert(delta->status <= GIT_DELTA_TYPECHANGE);
+	cl_assert(delta->status <= GIT_DELTA_CONFLICTED);
 
 	e->file_status[delta->status] += 1;
 
diff --git a/tests/diff/diff_helpers.h b/tests/diff/diff_helpers.h
index bf21f4b1f..6bcd1e671 100644
--- a/tests/diff/diff_helpers.h
+++ b/tests/diff/diff_helpers.h
@@ -8,7 +8,7 @@ typedef struct {
 	int files;
 	int files_binary;
 
-	int file_status[10]; /* indexed by git_delta_t value */
+	int file_status[11]; /* indexed by git_delta_t value */
 
 	int hunks;
 	int hunk_new_lines;
diff --git a/tests/diff/index.c b/tests/diff/index.c
index 21afe8da2..a544b83c7 100644
--- a/tests/diff/index.c
+++ b/tests/diff/index.c
@@ -163,3 +163,79 @@ void test_diff_index__checks_options_version(void)
 	git_tree_free(a);
 }
 
+static void do_conflicted_diff(diff_expects *exp, unsigned long flags)
+{
+	const char *a_commit = "26a125ee1bf"; /* the current HEAD */
+	git_tree *a = resolve_commit_oid_to_tree(g_repo, a_commit);
+	git_diff_options opts = GIT_DIFF_OPTIONS_INIT;
+	git_index_entry ancestor = {0}, ours = {0}, theirs = {0};
+	git_diff *diff = NULL;
+	git_index *index;
+
+	cl_assert(a);
+
+	opts.context_lines = 1;
+	opts.interhunk_lines = 1;
+	opts.flags |= flags;
+
+	memset(exp, 0, sizeof(diff_expects));
+
+	cl_git_pass(git_repository_index(&index, g_repo));
+
+	ancestor.path = ours.path = theirs.path = "staged_changes";
+	ancestor.mode = ours.mode = theirs.mode = 0100644;
+
+	git_oid_fromstr(&ancestor.id, "deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+	git_oid_fromstr(&ours.id, "deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+	git_oid_fromstr(&theirs.id, "deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+
+	cl_git_pass(git_index_conflict_add(index, &ancestor, &ours, &theirs));
+	cl_git_pass(git_diff_tree_to_index(&diff, g_repo, a, index, &opts));
+
+	cl_git_pass(git_diff_foreach(
+		diff, diff_file_cb, diff_hunk_cb, diff_line_cb, exp));
+
+	git_diff_free(diff);
+	git_tree_free(a);
+	git_index_free(index);
+}
+
+void test_diff_index__reports_conflicts(void)
+{
+	diff_expects exp;
+
+	do_conflicted_diff(&exp, 0);
+
+	cl_assert_equal_i(8, exp.files);
+	cl_assert_equal_i(3, exp.file_status[GIT_DELTA_ADDED]);
+	cl_assert_equal_i(2, exp.file_status[GIT_DELTA_DELETED]);
+	cl_assert_equal_i(2, exp.file_status[GIT_DELTA_MODIFIED]);
+	cl_assert_equal_i(1, exp.file_status[GIT_DELTA_CONFLICTED]);
+
+	cl_assert_equal_i(7, exp.hunks);
+
+	cl_assert_equal_i(9, exp.lines);
+	cl_assert_equal_i(2, exp.line_ctxt);
+	cl_assert_equal_i(5, exp.line_adds);
+	cl_assert_equal_i(2, exp.line_dels);
+}
+
+void test_diff_index__reports_conflicts_when_reversed(void)
+{
+	diff_expects exp;
+
+	do_conflicted_diff(&exp, GIT_DIFF_REVERSE);
+
+	cl_assert_equal_i(8, exp.files);
+	cl_assert_equal_i(2, exp.file_status[GIT_DELTA_ADDED]);
+	cl_assert_equal_i(3, exp.file_status[GIT_DELTA_DELETED]);
+	cl_assert_equal_i(2, exp.file_status[GIT_DELTA_MODIFIED]);
+	cl_assert_equal_i(1, exp.file_status[GIT_DELTA_CONFLICTED]);
+
+	cl_assert_equal_i(7, exp.hunks);
+
+	cl_assert_equal_i(9, exp.lines);
+	cl_assert_equal_i(2, exp.line_ctxt);
+	cl_assert_equal_i(2, exp.line_adds);
+	cl_assert_equal_i(5, exp.line_dels);
+}
diff --git a/tests/diff/workdir.c b/tests/diff/workdir.c
index 963be9481..460f1b592 100644
--- a/tests/diff/workdir.c
+++ b/tests/diff/workdir.c
@@ -68,6 +68,51 @@ void test_diff_workdir__to_index(void)
 	git_diff_free(diff);
 }
 
+void test_diff_workdir__to_index_with_conflicts(void)
+{
+	git_diff_options opts = GIT_DIFF_OPTIONS_INIT;
+	git_diff *diff = NULL;
+	git_index *index;
+	git_index_entry our_entry = {0}, their_entry = {0};
+	diff_expects exp = {0};
+
+	g_repo = cl_git_sandbox_init("status");
+
+	opts.context_lines = 3;
+	opts.interhunk_lines = 1;
+
+	/* Adding an entry that represents a rename gets two files in conflict */
+	our_entry.path = "subdir/modified_file";
+	our_entry.mode = 0100644;
+
+	their_entry.path = "subdir/rename_conflict";
+	their_entry.mode = 0100644;
+
+	cl_git_pass(git_repository_index(&index, g_repo));
+	cl_git_pass(git_index_conflict_add(index, NULL, &our_entry, &their_entry));
+
+	cl_git_pass(git_diff_index_to_workdir(&diff, g_repo, index, &opts));
+
+	cl_git_pass(diff_foreach_via_iterator(
+		diff, diff_file_cb, diff_hunk_cb, diff_line_cb, &exp));
+
+	cl_assert_equal_i(9, exp.files);
+	cl_assert_equal_i(0, exp.file_status[GIT_DELTA_ADDED]);
+	cl_assert_equal_i(4, exp.file_status[GIT_DELTA_DELETED]);
+	cl_assert_equal_i(3, exp.file_status[GIT_DELTA_MODIFIED]);
+	cl_assert_equal_i(2, exp.file_status[GIT_DELTA_CONFLICTED]);
+
+	cl_assert_equal_i(7, exp.hunks);
+
+	cl_assert_equal_i(12, exp.lines);
+	cl_assert_equal_i(4, exp.line_ctxt);
+	cl_assert_equal_i(3, exp.line_adds);
+	cl_assert_equal_i(5, exp.line_dels);
+
+	git_diff_free(diff);
+	git_index_free(index);
+}
+
 void test_diff_workdir__to_index_with_assume_unchanged(void)
 {
 	git_diff_options opts = GIT_DIFF_OPTIONS_INIT;
diff --git a/tests/index/addall.c b/tests/index/addall.c
index 377d2079e..211e76228 100644
--- a/tests/index/addall.c
+++ b/tests/index/addall.c
@@ -12,10 +12,7 @@ void test_index_addall__initialize(void)
 
 void test_index_addall__cleanup(void)
 {
-	git_repository_free(g_repo);
-	g_repo = NULL;
-
-	cl_fixture_cleanup(TEST_DIR);
+	cl_git_sandbox_cleanup();
 }
 
 #define STATUS_INDEX_FLAGS \
@@ -36,6 +33,7 @@ typedef struct {
 	size_t wt_dels;
 	size_t wt_mods;
 	size_t ignores;
+	size_t conflicts;
 } index_status_counts;
 
 static int index_status_cb(
@@ -67,6 +65,8 @@ static int index_status_cb(
 
 	if (status_flags & GIT_STATUS_IGNORED)
 		vals->ignores++;
+	if (status_flags & GIT_STATUS_CONFLICTED)
+		vals->conflicts++;
 
 	return 0;
 }
@@ -75,7 +75,7 @@ static void check_status_at_line(
 	git_repository *repo,
 	size_t index_adds, size_t index_dels, size_t index_mods,
 	size_t wt_adds, size_t wt_dels, size_t wt_mods, size_t ignores,
-	const char *file, int line)
+	size_t conflicts, const char *file, int line)
 {
 	index_status_counts vals;
 
@@ -97,10 +97,12 @@ static void check_status_at_line(
 		file,line,"wrong workdir mods", 1, "%"PRIuZ, wt_mods, vals.wt_mods);
 	clar__assert_equal(
 		file,line,"wrong ignores", 1, "%"PRIuZ, ignores, vals.ignores);
+	clar__assert_equal(
+		file,line,"wrong conflicts", 1, "%"PRIuZ, conflicts, vals.conflicts);
 }
 
-#define check_status(R,IA,ID,IM,WA,WD,WM,IG) \
-	check_status_at_line(R,IA,ID,IM,WA,WD,WM,IG,__FILE__,__LINE__)
+#define check_status(R,IA,ID,IM,WA,WD,WM,IG,C) \
+	check_status_at_line(R,IA,ID,IM,WA,WD,WM,IG,C,__FILE__,__LINE__)
 
 static void check_stat_data(git_index *index, const char *path, bool match)
 {
@@ -137,21 +139,22 @@ static void check_stat_data(git_index *index, const char *path, bool match)
 
 static void addall_create_test_repo(bool check_every_step)
 {
-	cl_git_pass(git_repository_init(&g_repo, TEST_DIR, false));
+	g_repo = cl_git_sandbox_init_new(TEST_DIR);
+
 	if (check_every_step)
-		check_status(g_repo, 0, 0, 0, 0, 0, 0, 0);
+		check_status(g_repo, 0, 0, 0, 0, 0, 0, 0, 0);
 
 	cl_git_mkfile(TEST_DIR "/file.foo", "a file");
 	if (check_every_step)
-		check_status(g_repo, 0, 0, 0, 1, 0, 0, 0);
+		check_status(g_repo, 0, 0, 0, 1, 0, 0, 0, 0);
 
 	cl_git_mkfile(TEST_DIR "/.gitignore", "*.foo\n");
 	if (check_every_step)
-		check_status(g_repo, 0, 0, 0, 1, 0, 0, 1);
+		check_status(g_repo, 0, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_mkfile(TEST_DIR "/file.bar", "another file");
 	if (check_every_step)
-		check_status(g_repo, 0, 0, 0, 2, 0, 0, 1);
+		check_status(g_repo, 0, 0, 0, 2, 0, 0, 1, 0);
 }
 
 void test_index_addall__repo_lifecycle(void)
@@ -171,107 +174,107 @@ void test_index_addall__repo_lifecycle(void)
 
 	cl_git_pass(git_index_add_all(index, &paths, 0, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.bar", true);
-	check_status(g_repo, 1, 0, 0, 1, 0, 0, 1);
+	check_status(g_repo, 1, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_rewritefile(TEST_DIR "/file.bar", "new content for file");
 	check_stat_data(index, TEST_DIR "/file.bar", false);
-	check_status(g_repo, 1, 0, 0, 1, 0, 1, 1);
+	check_status(g_repo, 1, 0, 0, 1, 0, 1, 1, 0);
 
 	cl_git_mkfile(TEST_DIR "/file.zzz", "yet another one");
 	cl_git_mkfile(TEST_DIR "/other.zzz", "yet another one");
 	cl_git_mkfile(TEST_DIR "/more.zzz", "yet another one");
-	check_status(g_repo, 1, 0, 0, 4, 0, 1, 1);
+	check_status(g_repo, 1, 0, 0, 4, 0, 1, 1, 0);
 
 	cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.bar", true);
-	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1);
+	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1, 0);
 
 	cl_git_pass(git_index_add_all(index, &paths, 0, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.zzz", true);
-	check_status(g_repo, 2, 0, 0, 3, 0, 0, 1);
+	check_status(g_repo, 2, 0, 0, 3, 0, 0, 1, 0);
 
 	cl_repo_commit_from_index(NULL, g_repo, NULL, 0, "first commit");
-	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1);
+	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1, 0);
 
 	if (cl_repo_get_bool(g_repo, "core.filemode")) {
 		cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
 		cl_must_pass(p_chmod(TEST_DIR "/file.zzz", 0777));
 		cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
-		check_status(g_repo, 0, 0, 1, 3, 0, 0, 1);
+		check_status(g_repo, 0, 0, 1, 3, 0, 0, 1, 0);
 
 		/* go back to what we had before */
 		cl_must_pass(p_chmod(TEST_DIR "/file.zzz", 0666));
 		cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
-		check_status(g_repo, 0, 0, 0, 3, 0, 0, 1);
+		check_status(g_repo, 0, 0, 0, 3, 0, 0, 1, 0);
 	}
 
 
 	/* attempt to add an ignored file - does nothing */
 	strs[0] = "file.foo";
 	cl_git_pass(git_index_add_all(index, &paths, 0, NULL, NULL));
-	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1);
+	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1, 0);
 
 	/* add with check - should generate error */
 	error = git_index_add_all(
 		index, &paths, GIT_INDEX_ADD_CHECK_PATHSPEC, NULL, NULL);
 	cl_assert_equal_i(GIT_EINVALIDSPEC, error);
-	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1);
+	check_status(g_repo, 0, 0, 0, 3, 0, 0, 1, 0);
 
 	/* add with force - should allow */
 	cl_git_pass(git_index_add_all(
 		index, &paths, GIT_INDEX_ADD_FORCE, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.foo", true);
-	check_status(g_repo, 1, 0, 0, 3, 0, 0, 0);
+	check_status(g_repo, 1, 0, 0, 3, 0, 0, 0, 0);
 
 	/* now it's in the index, so regular add should work */
 	cl_git_rewritefile(TEST_DIR "/file.foo", "new content for file");
 	check_stat_data(index, TEST_DIR "/file.foo", false);
-	check_status(g_repo, 1, 0, 0, 3, 0, 1, 0);
+	check_status(g_repo, 1, 0, 0, 3, 0, 1, 0, 0);
 
 	cl_git_pass(git_index_add_all(index, &paths, 0, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.foo", true);
-	check_status(g_repo, 1, 0, 0, 3, 0, 0, 0);
+	check_status(g_repo, 1, 0, 0, 3, 0, 0, 0, 0);
 
 	cl_git_pass(git_index_add_bypath(index, "more.zzz"));
 	check_stat_data(index, TEST_DIR "/more.zzz", true);
-	check_status(g_repo, 2, 0, 0, 2, 0, 0, 0);
+	check_status(g_repo, 2, 0, 0, 2, 0, 0, 0, 0);
 
 	cl_git_rewritefile(TEST_DIR "/file.zzz", "new content for file");
-	check_status(g_repo, 2, 0, 0, 2, 0, 1, 0);
+	check_status(g_repo, 2, 0, 0, 2, 0, 1, 0, 0);
 
 	cl_git_pass(git_index_add_bypath(index, "file.zzz"));
 	check_stat_data(index, TEST_DIR "/file.zzz", true);
-	check_status(g_repo, 2, 0, 1, 2, 0, 0, 0);
+	check_status(g_repo, 2, 0, 1, 2, 0, 0, 0, 0);
 
 	strs[0] = "*.zzz";
 	cl_git_pass(git_index_remove_all(index, &paths, NULL, NULL));
-	check_status(g_repo, 1, 1, 0, 4, 0, 0, 0);
+	check_status(g_repo, 1, 1, 0, 4, 0, 0, 0, 0);
 
 	cl_git_pass(git_index_add_bypath(index, "file.zzz"));
-	check_status(g_repo, 1, 0, 1, 3, 0, 0, 0);
+	check_status(g_repo, 1, 0, 1, 3, 0, 0, 0, 0);
 
 	cl_repo_commit_from_index(NULL, g_repo, NULL, 0, "second commit");
-	check_status(g_repo, 0, 0, 0, 3, 0, 0, 0);
+	check_status(g_repo, 0, 0, 0, 3, 0, 0, 0, 0);
 
 	cl_must_pass(p_unlink(TEST_DIR "/file.zzz"));
-	check_status(g_repo, 0, 0, 0, 3, 1, 0, 0);
+	check_status(g_repo, 0, 0, 0, 3, 1, 0, 0, 0);
 
 	/* update_all should be able to remove entries */
 	cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
-	check_status(g_repo, 0, 1, 0, 3, 0, 0, 0);
+	check_status(g_repo, 0, 1, 0, 3, 0, 0, 0, 0);
 
 	strs[0] = "*";
 	cl_git_pass(git_index_add_all(index, &paths, 0, NULL, NULL));
-	check_status(g_repo, 3, 1, 0, 0, 0, 0, 0);
+	check_status(g_repo, 3, 1, 0, 0, 0, 0, 0, 0);
 
 	/* must be able to remove at any position while still updating other files */
 	cl_must_pass(p_unlink(TEST_DIR "/.gitignore"));
 	cl_git_rewritefile(TEST_DIR "/file.zzz", "reconstructed file");
 	cl_git_rewritefile(TEST_DIR "/more.zzz", "altered file reality");
-	check_status(g_repo, 3, 1, 0, 1, 1, 1, 0);
+	check_status(g_repo, 3, 1, 0, 1, 1, 1, 0, 0);
 
 	cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
-	check_status(g_repo, 2, 1, 0, 1, 0, 0, 0);
+	check_status(g_repo, 2, 1, 0, 1, 0, 0, 0, 0);
 	/* this behavior actually matches 'git add -u' where "file.zzz" has
 	 * been removed from the index, so when you go to update, even though
 	 * it exists in the HEAD, it is not re-added to the index, leaving it
@@ -293,14 +296,14 @@ void test_index_addall__files_in_folders(void)
 
 	cl_git_pass(git_index_add_all(index, NULL, 0, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.bar", true);
-	check_status(g_repo, 2, 0, 0, 0, 0, 0, 1);
+	check_status(g_repo, 2, 0, 0, 0, 0, 0, 1, 0);
 
 	cl_must_pass(p_mkdir(TEST_DIR "/subdir", 0777));
 	cl_git_mkfile(TEST_DIR "/subdir/file", "hello!\n");
-	check_status(g_repo, 2, 0, 0, 1, 0, 0, 1);
+	check_status(g_repo, 2, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_pass(git_index_add_all(index, NULL, 0, NULL, NULL));
-	check_status(g_repo, 3, 0, 0, 0, 0, 0, 1);
+	check_status(g_repo, 3, 0, 0, 0, 0, 0, 1, 0);
 
 	git_index_free(index);
 }
@@ -337,7 +340,7 @@ void test_index_addall__callback_filtering(void)
 	cl_git_pass(
 		git_index_add_all(index, NULL, 0, addall_match_prefix, "file."));
 	check_stat_data(index, TEST_DIR "/file.bar", true);
-	check_status(g_repo, 1, 0, 0, 1, 0, 0, 1);
+	check_status(g_repo, 1, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_mkfile(TEST_DIR "/file.zzz", "yet another one");
 	cl_git_mkfile(TEST_DIR "/more.zzz", "yet another one");
@@ -345,32 +348,32 @@ void test_index_addall__callback_filtering(void)
 
 	cl_git_pass(git_index_update_all(index, NULL, NULL, NULL));
 	check_stat_data(index, TEST_DIR "/file.bar", true);
-	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1);
+	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1, 0);
 
 	cl_git_pass(
 		git_index_add_all(index, NULL, 0, addall_match_prefix, "other"));
 	check_stat_data(index, TEST_DIR "/other.zzz", true);
-	check_status(g_repo, 2, 0, 0, 3, 0, 0, 1);
+	check_status(g_repo, 2, 0, 0, 3, 0, 0, 1, 0);
 
 	cl_git_pass(
 		git_index_add_all(index, NULL, 0, addall_match_suffix, ".zzz"));
-	check_status(g_repo, 4, 0, 0, 1, 0, 0, 1);
+	check_status(g_repo, 4, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_pass(
 		git_index_remove_all(index, NULL, addall_match_suffix, ".zzz"));
-	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1);
+	check_status(g_repo, 1, 0, 0, 4, 0, 0, 1, 0);
 
 	cl_git_fail_with(
 		git_index_add_all(index, NULL, 0, addall_cancel_at, "more.zzz"), -123);
-	check_status(g_repo, 3, 0, 0, 2, 0, 0, 1);
+	check_status(g_repo, 3, 0, 0, 2, 0, 0, 1, 0);
 
 	cl_git_fail_with(
 		git_index_add_all(index, NULL, 0, addall_cancel_at, "other.zzz"), -123);
-	check_status(g_repo, 4, 0, 0, 1, 0, 0, 1);
+	check_status(g_repo, 4, 0, 0, 1, 0, 0, 1, 0);
 
 	cl_git_pass(
 		git_index_add_all(index, NULL, 0, addall_match_suffix, ".zzz"));
-	check_status(g_repo, 5, 0, 0, 0, 0, 0, 1);
+	check_status(g_repo, 5, 0, 0, 0, 0, 0, 1, 0);
 
 	cl_must_pass(p_unlink(TEST_DIR "/file.zzz"));
 	cl_must_pass(p_unlink(TEST_DIR "/more.zzz"));
@@ -380,13 +383,65 @@ void test_index_addall__callback_filtering(void)
 		git_index_update_all(index, NULL, addall_cancel_at, "more.zzz"), -123);
 	/* file.zzz removed from index (so Index Adds 5 -> 4) and
 	 * more.zzz + other.zzz removed (so Worktree Dels 0 -> 2) */
-	check_status(g_repo, 4, 0, 0, 0, 2, 0, 1);
+	check_status(g_repo, 4, 0, 0, 0, 2, 0, 1, 0);
 
 	cl_git_fail_with(
 		git_index_update_all(index, NULL, addall_cancel_at, "other.zzz"), -123);
 	/* more.zzz removed from index (so Index Adds 4 -> 3) and
 	 * Just other.zzz removed (so Worktree Dels 2 -> 1) */
-	check_status(g_repo, 3, 0, 0, 0, 1, 0, 1);
+	check_status(g_repo, 3, 0, 0, 0, 1, 0, 1, 0);
 
 	git_index_free(index);
 }
+
+void test_index_addall__adds_conflicts(void)
+{
+	git_index *index;
+	git_reference *ref;
+	git_annotated_commit *annotated;
+
+	g_repo = cl_git_sandbox_init("merge-resolve");
+	cl_git_pass(git_repository_index(&index, g_repo));
+
+	check_status(g_repo, 0, 0, 0, 0, 0, 0, 0, 0);
+
+	cl_git_pass(git_reference_lookup(&ref, g_repo, "refs/heads/branch"));
+	cl_git_pass(git_annotated_commit_from_ref(&annotated, g_repo, ref));
+
+	cl_git_pass(git_merge(g_repo, &annotated, 1, NULL, NULL));
+	check_status(g_repo, 0, 1, 2, 0, 0, 0, 0, 1);
+
+	cl_git_pass(git_index_add_all(index, NULL, 0, NULL, NULL));
+	check_status(g_repo, 0, 1, 3, 0, 0, 0, 0, 0);
+
+	git_annotated_commit_free(annotated);
+	git_reference_free(ref);
+	git_index_free(index);
+}
+
+void test_index_addall__removes_deleted_conflicted_files(void)
+{
+	git_index *index;
+	git_reference *ref;
+	git_annotated_commit *annotated;
+
+	g_repo = cl_git_sandbox_init("merge-resolve");
+	cl_git_pass(git_repository_index(&index, g_repo));
+
+	check_status(g_repo, 0, 0, 0, 0, 0, 0, 0, 0);
+
+	cl_git_pass(git_reference_lookup(&ref, g_repo, "refs/heads/branch"));
+	cl_git_pass(git_annotated_commit_from_ref(&annotated, g_repo, ref));
+
+	cl_git_pass(git_merge(g_repo, &annotated, 1, NULL, NULL));
+	check_status(g_repo, 0, 1, 2, 0, 0, 0, 0, 1);
+
+	cl_git_rmfile("merge-resolve/conflicting.txt");
+
+	cl_git_pass(git_index_add_all(index, NULL, 0, NULL, NULL));
+	check_status(g_repo, 0, 2, 2, 0, 0, 0, 0, 0);
+
+	git_annotated_commit_free(annotated);
+	git_reference_free(ref);
+	git_index_free(index);
+}
\ No newline at end of file
diff --git a/tests/index/collision.c b/tests/index/collision.c
index 1f002e8d3..19c1548e9 100644
--- a/tests/index/collision.c
+++ b/tests/index/collision.c
@@ -57,7 +57,7 @@ void test_index_collision__add_with_highstage_1(void)
 	git_oid_fromstr(&entry.id, "e69de29bb2d1d6434b8b29ae775ad8c2e48c5391");
 
 	entry.path = "a/b";
-	entry.flags = (2 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 2);
 	cl_git_pass(git_index_add(index, &entry));
 
 	/* create a blob beneath the previous tree entry */
@@ -67,7 +67,7 @@ void test_index_collision__add_with_highstage_1(void)
 
 	/* create another tree entry above the blob */
 	entry.path = "a/b";
-	entry.flags = (1 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 1);
 	cl_git_pass(git_index_add(index, &entry));
 
 	git_index_free(index);
@@ -89,17 +89,17 @@ void test_index_collision__add_with_highstage_2(void)
 	git_oid_fromstr(&entry.id, "e69de29bb2d1d6434b8b29ae775ad8c2e48c5391");
 
 	entry.path = "a/b/c";
-	entry.flags = (1 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 1);
 	cl_git_pass(git_index_add(index, &entry));
 
 	/* create a blob beneath the previous tree entry */
 	entry.path = "a/b/c";
-	entry.flags = (2 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 2);
 	cl_git_pass(git_index_add(index, &entry));
 
 	/* create another tree entry above the blob */
 	entry.path = "a/b";
-	entry.flags = (3 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, 3);
 	cl_git_pass(git_index_add(index, &entry));
 
 	git_index_free(index);
diff --git a/tests/index/conflicts.c b/tests/index/conflicts.c
index 427351693..b7a2456eb 100644
--- a/tests/index/conflicts.c
+++ b/tests/index/conflicts.c
@@ -16,6 +16,7 @@ static git_index *repo_index;
 #define CONFLICTS_TWO_OUR_OID "8b3f43d2402825c200f835ca1762413e386fd0b2"
 #define CONFLICTS_TWO_THEIR_OID "220bd62631c8cf7a83ef39c6b94595f00517211e"
 
+#define TEST_STAGED_OID "beefdadafeedabedcafedeedbabedeadbeaddeaf"
 #define TEST_ANCESTOR_OID "f00ff00ff00ff00ff00ff00ff00ff00ff00ff00f"
 #define TEST_OUR_OID "b44bb44bb44bb44bb44bb44bb44bb44bb44bb44b"
 #define TEST_THEIR_OID "0123456789abcdef0123456789abcdef01234567"
@@ -46,15 +47,18 @@ void test_index_conflicts__add(void)
 	memset(&their_entry, 0x0, sizeof(git_index_entry));
 
 	ancestor_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (1 << GIT_IDXENTRY_STAGESHIFT);
+	ancestor_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 1);
 	git_oid_fromstr(&ancestor_entry.id, TEST_ANCESTOR_OID);
 
 	our_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (2 << GIT_IDXENTRY_STAGESHIFT);
+	our_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&our_entry, 2);
 	git_oid_fromstr(&our_entry.id, TEST_OUR_OID);
 
 	their_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (3 << GIT_IDXENTRY_STAGESHIFT);
+	their_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 2);
 	git_oid_fromstr(&their_entry.id, TEST_THEIR_OID);
 
 	cl_git_pass(git_index_conflict_add(repo_index, &ancestor_entry, &our_entry, &their_entry));
@@ -74,15 +78,18 @@ void test_index_conflicts__add_fixes_incorrect_stage(void)
 	memset(&their_entry, 0x0, sizeof(git_index_entry));
 
 	ancestor_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (3 << GIT_IDXENTRY_STAGESHIFT);
+	ancestor_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 3);
 	git_oid_fromstr(&ancestor_entry.id, TEST_ANCESTOR_OID);
 
 	our_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (1 << GIT_IDXENTRY_STAGESHIFT);
+	our_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&our_entry, 1);
 	git_oid_fromstr(&our_entry.id, TEST_OUR_OID);
 
 	their_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (2 << GIT_IDXENTRY_STAGESHIFT);
+	their_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&their_entry, 2);
 	git_oid_fromstr(&their_entry.id, TEST_THEIR_OID);
 
 	cl_git_pass(git_index_conflict_add(repo_index, &ancestor_entry, &our_entry, &their_entry));
@@ -96,6 +103,55 @@ void test_index_conflicts__add_fixes_incorrect_stage(void)
 	cl_assert(git_index_entry_stage(conflict_entry[2]) == 3);
 }
 
+void test_index_conflicts__add_removes_stage_zero(void)
+{
+	git_index_entry staged, ancestor_entry, our_entry, their_entry;
+	const git_index_entry *conflict_entry[3];
+
+	cl_assert(git_index_entrycount(repo_index) == 8);
+
+	memset(&staged, 0x0, sizeof(git_index_entry));
+	memset(&ancestor_entry, 0x0, sizeof(git_index_entry));
+	memset(&our_entry, 0x0, sizeof(git_index_entry));
+	memset(&their_entry, 0x0, sizeof(git_index_entry));
+
+	staged.path = "test-one.txt";
+	staged.mode = 0100644;
+	git_oid_fromstr(&staged.id, TEST_STAGED_OID);
+	cl_git_pass(git_index_add(repo_index, &staged));
+	cl_assert(git_index_entrycount(repo_index) == 9);
+
+	ancestor_entry.path = "test-one.txt";
+	ancestor_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 3);
+	git_oid_fromstr(&ancestor_entry.id, TEST_ANCESTOR_OID);
+
+	our_entry.path = "test-one.txt";
+	our_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&our_entry, 1);
+	git_oid_fromstr(&our_entry.id, TEST_OUR_OID);
+
+	their_entry.path = "test-one.txt";
+	their_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&their_entry, 2);
+	git_oid_fromstr(&their_entry.id, TEST_THEIR_OID);
+
+	cl_git_pass(git_index_conflict_add(repo_index, &ancestor_entry, &our_entry, &their_entry));
+
+	cl_assert(git_index_entrycount(repo_index) == 11);
+
+	cl_assert_equal_p(NULL, git_index_get_bypath(repo_index, "test-one.txt", 0));
+
+	cl_git_pass(git_index_conflict_get(&conflict_entry[0], &conflict_entry[1], &conflict_entry[2], repo_index, "test-one.txt"));
+
+	cl_assert_equal_oid(&ancestor_entry.id, &conflict_entry[0]->id);
+	cl_assert_equal_i(1, git_index_entry_stage(conflict_entry[0]));
+	cl_assert_equal_oid(&our_entry.id, &conflict_entry[1]->id);
+	cl_assert_equal_i(2, git_index_entry_stage(conflict_entry[1]));
+	cl_assert_equal_oid(&their_entry.id, &conflict_entry[2]->id);
+	cl_assert_equal_i(3, git_index_entry_stage(conflict_entry[2]));
+}
+
 void test_index_conflicts__get(void)
 {
 	const git_index_entry *conflict_entry[3];
@@ -216,7 +272,7 @@ void test_index_conflicts__moved_to_reuc_on_add(void)
 		cl_assert(entry = git_index_get_byindex(repo_index, i));
 
 		if (strcmp(entry->path, "conflicts-one.txt") == 0)
-			cl_assert(git_index_entry_stage(entry) == 0);
+			cl_assert(!git_index_entry_is_conflict(entry));
 	}
 }
 
@@ -256,7 +312,7 @@ void test_index_conflicts__remove_all_conflicts(void)
 
 	for (i = 0; i < git_index_entrycount(repo_index); i++) {
 		cl_assert(entry = git_index_get_byindex(repo_index, i));
-		cl_assert(git_index_entry_stage(entry) == 0);
+		cl_assert(!git_index_entry_is_conflict(entry));
 	}
 }
 
@@ -272,7 +328,8 @@ void test_index_conflicts__partial(void)
 	memset(&their_entry, 0x0, sizeof(git_index_entry));
 
 	ancestor_entry.path = "test-one.txt";
-	ancestor_entry.flags |= (1 << GIT_IDXENTRY_STAGESHIFT);
+	ancestor_entry.mode = 0100644;
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 1);
 	git_oid_fromstr(&ancestor_entry.id, TEST_ANCESTOR_OID);
 
 	cl_git_pass(git_index_conflict_add(repo_index, &ancestor_entry, NULL, NULL));
diff --git a/tests/merge/trees/trivial.c b/tests/merge/trees/trivial.c
index 55f38248f..2262edda6 100644
--- a/tests/merge/trees/trivial.c
+++ b/tests/merge/trees/trivial.c
@@ -71,7 +71,7 @@ static int merge_trivial_conflict_entrycount(git_index *index)
 	for (i = 0; i < git_index_entrycount(index); i++) {
 		cl_assert(entry = git_index_get_byindex(index, i));
 
-		if (git_index_entry_stage(entry) > 0)
+		if (git_index_entry_is_conflict(entry))
 			count++;
 	}
 
diff --git a/tests/merge/workdir/trivial.c b/tests/merge/workdir/trivial.c
index 5cc20f746..4ddaf233d 100644
--- a/tests/merge/workdir/trivial.c
+++ b/tests/merge/workdir/trivial.c
@@ -66,7 +66,7 @@ static size_t merge_trivial_conflict_entrycount(void)
 	for (i = 0; i < git_index_entrycount(repo_index); i++) {
 		cl_assert(entry = git_index_get_byindex(repo_index, i));
 
-		if (git_index_entry_stage(entry) > 0)
+		if (git_index_entry_is_conflict(entry))
 			count++;
 	}
 
diff --git a/tests/object/tree/duplicateentries.c b/tests/object/tree/duplicateentries.c
index 65be12e9b..35dd383ec 100644
--- a/tests/object/tree/duplicateentries.c
+++ b/tests/object/tree/duplicateentries.c
@@ -126,17 +126,17 @@ static void add_fake_conflicts(git_index *index)
 
 	ancestor_entry.path = "duplicate";
 	ancestor_entry.mode = GIT_FILEMODE_BLOB;
-	ancestor_entry.flags |= (1 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&ancestor_entry, 1);
 	git_oid_fromstr(&ancestor_entry.id, "a8233120f6ad708f843d861ce2b7228ec4e3dec6");
 
 	our_entry.path = "duplicate";
 	our_entry.mode = GIT_FILEMODE_BLOB;
-	ancestor_entry.flags |= (2 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&our_entry, 2);
 	git_oid_fromstr(&our_entry.id, "45b983be36b73c0788dc9cbcb76cbb80fc7bb057");
 
 	their_entry.path = "duplicate";
 	their_entry.mode = GIT_FILEMODE_BLOB;
-	ancestor_entry.flags |= (3 << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&their_entry, 3);
 	git_oid_fromstr(&their_entry.id, "a71586c1dfe8a71c6cbf6c129f404c5642ff31bd");
 
 	cl_git_pass(git_index_conflict_add(index, &ancestor_entry, &our_entry, &their_entry));
diff --git a/tests/reset/hard.c b/tests/reset/hard.c
index 86d4be2ed..88055adda 100644
--- a/tests/reset/hard.c
+++ b/tests/reset/hard.c
@@ -108,7 +108,7 @@ static void index_entry_init(git_index *index, int side, git_oid *oid)
 	memset(&entry, 0x0, sizeof(git_index_entry));
 
 	entry.path = "conflicting_file";
-	entry.flags = (side << GIT_IDXENTRY_STAGESHIFT);
+	GIT_IDXENTRY_STAGE_SET(&entry, side);
 	entry.mode = 0100644;
 	git_oid_cpy(&entry.id, oid);
 
diff --git a/tests/status/worktree.c b/tests/status/worktree.c
index 8897bf9b5..e272c0a10 100644
--- a/tests/status/worktree.c
+++ b/tests/status/worktree.c
@@ -461,14 +461,17 @@ void test_status_worktree__conflict_with_diff3(void)
 	memset(&their_entry, 0x0, sizeof(git_index_entry));
 
 	ancestor_entry.path = "modified_file";
+	ancestor_entry.mode = 0100644;
 	git_oid_fromstr(&ancestor_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
 
 	our_entry.path = "modified_file";
+	our_entry.mode = 0100644;
 	git_oid_fromstr(&our_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
 
 	their_entry.path = "modified_file";
+	their_entry.mode = 0100644;
 	git_oid_fromstr(&their_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
 
@@ -484,7 +487,7 @@ void test_status_worktree__conflict_with_diff3(void)
 
 	cl_git_pass(git_status_file(&status, repo, "modified_file"));
 
-	cl_assert_equal_i(GIT_STATUS_INDEX_DELETED | GIT_STATUS_WT_NEW, status);
+	cl_assert_equal_i(GIT_STATUS_CONFLICTED, status);
 }
 
 static const char *filemode_paths[] = {
@@ -614,14 +617,17 @@ void test_status_worktree__conflicted_item(void)
 	memset(&our_entry, 0x0, sizeof(git_index_entry));
 	memset(&their_entry, 0x0, sizeof(git_index_entry));
 
+	ancestor_entry.mode = 0100644;
 	ancestor_entry.path = "modified_file";
 	git_oid_fromstr(&ancestor_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
 
+	our_entry.mode = 0100644;
 	our_entry.path = "modified_file";
 	git_oid_fromstr(&our_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
 
+	their_entry.mode = 0100644;
 	their_entry.path = "modified_file";
 	git_oid_fromstr(&their_entry.id,
 		"452e4244b5d083ddf0460acf1ecc74db9dcfa11a");
@@ -634,9 +640,55 @@ void test_status_worktree__conflicted_item(void)
 		&our_entry, &their_entry));
 
 	cl_git_pass(git_status_file(&status, repo, "modified_file"));
-	cl_assert_equal_i(GIT_STATUS_WT_MODIFIED, status);
+	cl_assert_equal_i(GIT_STATUS_CONFLICTED, status);
+
+	git_index_free(index);
+}
+
+void test_status_worktree__conflict_has_no_oid(void)
+{
+	git_repository *repo = cl_git_sandbox_init("status");
+	git_index *index;
+	git_index_entry entry = {0};
+	git_status_list *statuslist;
+	const git_status_entry *status;
+	git_oid zero_id = {0};
+
+	entry.mode = 0100644;
+	entry.path = "modified_file";
+	git_oid_fromstr(&entry.id, "deadbeefdeadbeefdeadbeefdeadbeefdeadbeef");
+
+	cl_git_pass(git_repository_index(&index, repo));
+	cl_git_pass(git_index_conflict_add(index, &entry, &entry, &entry));
+
+	git_status_list_new(&statuslist, repo, NULL);
+
+	cl_assert_equal_i(16, git_status_list_entrycount(statuslist));
+
+	status = git_status_byindex(statuslist, 2);
+
+	cl_assert_equal_i(GIT_STATUS_CONFLICTED, status->status);
+	cl_assert_equal_s("modified_file", status->head_to_index->old_file.path);
+	cl_assert(!git_oid_equal(&zero_id, &status->head_to_index->old_file.id));
+	cl_assert(0 != status->head_to_index->old_file.mode);
+	cl_assert_equal_s("modified_file", status->head_to_index->new_file.path);
+	cl_assert_equal_oid(&zero_id, &status->head_to_index->new_file.id);
+	cl_assert_equal_i(0, status->head_to_index->new_file.mode);
+	cl_assert_equal_i(0, status->head_to_index->new_file.size);
+
+	cl_assert_equal_s("modified_file", status->index_to_workdir->old_file.path);
+	cl_assert_equal_oid(&zero_id, &status->index_to_workdir->old_file.id);
+	cl_assert_equal_i(0, status->index_to_workdir->old_file.mode);
+	cl_assert_equal_i(0, status->index_to_workdir->old_file.size);
+	cl_assert_equal_s("modified_file", status->index_to_workdir->new_file.path);
+	cl_assert(
+		!git_oid_equal(&zero_id, &status->index_to_workdir->new_file.id) ||
+		!(status->index_to_workdir->new_file.flags & GIT_DIFF_FLAG_VALID_ID));
+	cl_assert(0 != status->index_to_workdir->new_file.mode);
+	cl_assert(0 != status->index_to_workdir->new_file.size);
 
 	git_index_free(index);
+	git_status_list_free(statuslist);
 }
 
 static void stage_and_commit(git_repository *repo, const char *path)