diff --git a/builtin/am.c b/builtin/am.c
index e4a0ff9cd7c..1ee70692bc3 100644
--- a/builtin/am.c
+++ b/builtin/am.c
@@ -1918,6 +1918,9 @@ static int fast_forward_to(struct tree *head, struct tree *remote, int reset)
 	opts.update = 1;
 	opts.merge = 1;
 	opts.reset = reset;
+	if (!reset)
+		/* FIXME: Default should be to remove ignored files */
+		opts.preserve_ignored = 1;
 	opts.fn = twoway_merge;
 	init_tree_desc(&t[0], head->buffer, head->size);
 	init_tree_desc(&t[1], remote->buffer, remote->size);
diff --git a/builtin/checkout.c b/builtin/checkout.c
index 5335435d616..5e7957dd068 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -648,6 +648,7 @@ static int reset_tree(struct tree *tree, const struct checkout_opts *o,
 	opts.skip_unmerged = !worktree;
 	opts.reset = 1;
 	opts.merge = 1;
+	opts.preserve_ignored = 0;
 	opts.fn = oneway_merge;
 	opts.verbose_update = o->show_progress;
 	opts.src_index = &the_index;
@@ -746,11 +747,7 @@ static int merge_working_tree(const struct checkout_opts *opts,
 				       new_branch_info->commit ?
 				       &new_branch_info->commit->object.oid :
 				       &new_branch_info->oid, NULL);
-		if (opts->overwrite_ignore) {
-			topts.dir = xcalloc(1, sizeof(*topts.dir));
-			topts.dir->flags |= DIR_SHOW_IGNORED;
-			setup_standard_excludes(topts.dir);
-		}
+		topts.preserve_ignored = !opts->overwrite_ignore;
 		tree = parse_tree_indirect(old_branch_info->commit ?
 					   &old_branch_info->commit->object.oid :
 					   the_hash_algo->empty_tree);
@@ -760,10 +757,6 @@ static int merge_working_tree(const struct checkout_opts *opts,
 		init_tree_desc(&trees[1], tree->buffer, tree->size);
 
 		ret = unpack_trees(2, trees, &topts);
-		if (topts.dir) {
-			dir_clear(topts.dir);
-			FREE_AND_NULL(topts.dir);
-		}
 		clear_unpack_trees_porcelain(&topts);
 		if (ret == -1) {
 			/*
diff --git a/builtin/clone.c b/builtin/clone.c
index ff1d3d447a3..be1c3840d62 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -687,6 +687,8 @@ static int checkout(int submodule_progress)
 	opts.update = 1;
 	opts.merge = 1;
 	opts.clone = 1;
+	/* FIXME: Default should be to remove ignored files */
+	opts.preserve_ignored = 1;
 	opts.fn = oneway_merge;
 	opts.verbose_update = (option_verbosity >= 0);
 	opts.src_index = &the_index;
diff --git a/builtin/merge.c b/builtin/merge.c
index 3fbdacc7db4..1e5fff095fc 100644
--- a/builtin/merge.c
+++ b/builtin/merge.c
@@ -680,6 +680,8 @@ static int read_tree_trivial(struct object_id *common, struct object_id *head,
 	opts.verbose_update = 1;
 	opts.trivial_merges_only = 1;
 	opts.merge = 1;
+	/* FIXME: Default should be to remove ignored files */
+	opts.preserve_ignored = 1;
 	trees[nr_trees] = parse_tree_indirect(common);
 	if (!trees[nr_trees++])
 		return -1;
diff --git a/builtin/read-tree.c b/builtin/read-tree.c
index 73cb957a69b..443d206eca6 100644
--- a/builtin/read-tree.c
+++ b/builtin/read-tree.c
@@ -201,11 +201,9 @@ int cmd_read_tree(int argc, const char **argv, const char *cmd_prefix)
 	if ((opts.update || opts.index_only) && !opts.merge)
 		die("%s is meaningless without -m, --reset, or --prefix",
 		    opts.update ? "-u" : "-i");
-	if (opts.update && !opts.reset) {
-		CALLOC_ARRAY(opts.dir, 1);
-		opts.dir->flags |= DIR_SHOW_IGNORED;
-		setup_standard_excludes(opts.dir);
-	}
+	if (opts.update && !opts.reset)
+		opts.preserve_ignored = 0;
+	/* otherwise, opts.preserve_ignored is irrelevant */
 	if (opts.merge && !opts.index_only)
 		setup_work_tree();
 
@@ -245,11 +243,6 @@ int cmd_read_tree(int argc, const char **argv, const char *cmd_prefix)
 	if (unpack_trees(nr_trees, t, &opts))
 		return 128;
 
-	if (opts.dir) {
-		dir_clear(opts.dir);
-		FREE_AND_NULL(opts.dir);
-	}
-
 	if (opts.debug_unpack || opts.dry_run)
 		return 0; /* do not write the index out */
 
diff --git a/builtin/reset.c b/builtin/reset.c
index 51c9e2f43ff..7f38656f018 100644
--- a/builtin/reset.c
+++ b/builtin/reset.c
@@ -67,6 +67,8 @@ static int reset_index(const char *ref, const struct object_id *oid, int reset_t
 	case KEEP:
 	case MERGE:
 		opts.update = 1;
+		/* FIXME: Default should be to remove ignored files */
+		opts.preserve_ignored = 1;
 		break;
 	case HARD:
 		opts.update = 1;
diff --git a/builtin/stash.c b/builtin/stash.c
index 8f42360ca91..88287b890d5 100644
--- a/builtin/stash.c
+++ b/builtin/stash.c
@@ -258,6 +258,9 @@ static int reset_tree(struct object_id *i_tree, int update, int reset)
 	opts.merge = 1;
 	opts.reset = reset;
 	opts.update = update;
+	if (update && !reset)
+		/* FIXME: Default should be to remove ignored files */
+		opts.preserve_ignored = 1;
 	opts.fn = oneway_merge;
 
 	if (unpack_trees(nr_trees, t, &opts))
diff --git a/merge-ort.c b/merge-ort.c
index 35aa979c3a4..0d64ec716bd 100644
--- a/merge-ort.c
+++ b/merge-ort.c
@@ -4045,11 +4045,7 @@ static int checkout(struct merge_options *opt,
 	unpack_opts.quiet = 0; /* FIXME: sequencer might want quiet? */
 	unpack_opts.verbose_update = (opt->verbosity > 2);
 	unpack_opts.fn = twoway_merge;
-	if (1/* FIXME: opts->overwrite_ignore*/) {
-		CALLOC_ARRAY(unpack_opts.dir, 1);
-		unpack_opts.dir->flags |= DIR_SHOW_IGNORED;
-		setup_standard_excludes(unpack_opts.dir);
-	}
+	unpack_opts.preserve_ignored = 0; /* FIXME: !opts->overwrite_ignore*/
 	parse_tree(prev);
 	init_tree_desc(&trees[0], prev->buffer, prev->size);
 	parse_tree(next);
@@ -4057,8 +4053,6 @@ static int checkout(struct merge_options *opt,
 
 	ret = unpack_trees(2, trees, &unpack_opts);
 	clear_unpack_trees_porcelain(&unpack_opts);
-	dir_clear(unpack_opts.dir);
-	FREE_AND_NULL(unpack_opts.dir);
 	return ret;
 }
 
diff --git a/merge-recursive.c b/merge-recursive.c
index 233d9f686ad..2be3f5d4044 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -411,9 +411,7 @@ static int unpack_trees_start(struct merge_options *opt,
 	else {
 		opt->priv->unpack_opts.update = 1;
 		/* FIXME: should only do this if !overwrite_ignore */
-		CALLOC_ARRAY(opt->priv->unpack_opts.dir, 1);
-		opt->priv->unpack_opts.dir->flags |= DIR_SHOW_IGNORED;
-		setup_standard_excludes(opt->priv->unpack_opts.dir);
+		opt->priv->unpack_opts.preserve_ignored = 0;
 	}
 	opt->priv->unpack_opts.merge = 1;
 	opt->priv->unpack_opts.head_idx = 2;
@@ -428,10 +426,6 @@ static int unpack_trees_start(struct merge_options *opt,
 	init_tree_desc_from_tree(t+2, merge);
 
 	rc = unpack_trees(3, t, &opt->priv->unpack_opts);
-	if (opt->priv->unpack_opts.dir) {
-		dir_clear(opt->priv->unpack_opts.dir);
-		FREE_AND_NULL(opt->priv->unpack_opts.dir);
-	}
 	cache_tree_free(&opt->repo->index->cache_tree);
 
 	/*
diff --git a/merge.c b/merge.c
index 6e736881d90..2382ff66d35 100644
--- a/merge.c
+++ b/merge.c
@@ -53,7 +53,6 @@ int checkout_fast_forward(struct repository *r,
 	struct unpack_trees_options opts;
 	struct tree_desc t[MAX_UNPACK_TREES];
 	int i, nr_trees = 0;
-	struct dir_struct dir = DIR_INIT;
 	struct lock_file lock_file = LOCK_INIT;
 
 	refresh_index(r->index, REFRESH_QUIET, NULL, NULL, NULL);
@@ -80,11 +79,7 @@ int checkout_fast_forward(struct repository *r,
 	}
 
 	memset(&opts, 0, sizeof(opts));
-	if (overwrite_ignore) {
-		dir.flags |= DIR_SHOW_IGNORED;
-		setup_standard_excludes(&dir);
-		opts.dir = &dir;
-	}
+	opts.preserve_ignored = !overwrite_ignore;
 
 	opts.head_idx = 1;
 	opts.src_index = r->index;
@@ -101,7 +96,6 @@ int checkout_fast_forward(struct repository *r,
 		clear_unpack_trees_porcelain(&opts);
 		return -1;
 	}
-	dir_clear(&dir);
 	clear_unpack_trees_porcelain(&opts);
 
 	if (write_locked_index(r->index, &lock_file, COMMIT_LOCK))
diff --git a/reset.c b/reset.c
index 79310ae071b..41b3e2d88de 100644
--- a/reset.c
+++ b/reset.c
@@ -56,6 +56,8 @@ int reset_head(struct repository *r, struct object_id *oid, const char *action,
 	unpack_tree_opts.fn = reset_hard ? oneway_merge : twoway_merge;
 	unpack_tree_opts.update = 1;
 	unpack_tree_opts.merge = 1;
+	/* FIXME: Default should be to remove ignored files */
+	unpack_tree_opts.preserve_ignored = 1;
 	init_checkout_metadata(&unpack_tree_opts.meta, switch_to_branch, oid, NULL);
 	if (!detach_head)
 		unpack_tree_opts.reset = 1;
diff --git a/sequencer.c b/sequencer.c
index 614d56f5e21..098566c68d9 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -3699,6 +3699,8 @@ static int do_reset(struct repository *r,
 	unpack_tree_opts.fn = oneway_merge;
 	unpack_tree_opts.merge = 1;
 	unpack_tree_opts.update = 1;
+	/* FIXME: Default should be to remove ignored files */
+	unpack_tree_opts.preserve_ignored = 1;
 	init_checkout_metadata(&unpack_tree_opts.meta, name, &oid, NULL);
 
 	if (repo_read_index_unmerged(r)) {
diff --git a/unpack-trees.c b/unpack-trees.c
index 8ea0a542da8..1e4eae1dc7d 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -1707,6 +1707,12 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 		ensure_full_index(o->dst_index);
 	}
 
+	if (!o->preserve_ignored) {
+		CALLOC_ARRAY(o->dir, 1);
+		o->dir->flags |= DIR_SHOW_IGNORED;
+		setup_standard_excludes(o->dir);
+	}
+
 	if (!core_apply_sparse_checkout || !o->update)
 		o->skip_sparse_checkout = 1;
 	if (!o->skip_sparse_checkout && !o->pl) {
@@ -1868,6 +1874,10 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 done:
 	if (free_pattern_list)
 		clear_pattern_list(&pl);
+	if (o->dir) {
+		dir_clear(o->dir);
+		FREE_AND_NULL(o->dir);
+	}
 	trace2_region_leave("unpack_trees", "unpack_trees", the_repository);
 	trace_performance_leave("unpack_trees");
 	return ret;
diff --git a/unpack-trees.h b/unpack-trees.h
index 2d88b19dca7..f98cfd49d7b 100644
--- a/unpack-trees.h
+++ b/unpack-trees.h
@@ -49,6 +49,7 @@ struct unpack_trees_options {
 	unsigned int reset,
 		     merge,
 		     update,
+		     preserve_ignored,
 		     clone,
 		     index_only,
 		     nontrivial_merge,
