Merge branch 'en/removing-untracked-fixes'

Various fixes in code paths that move untracked files away to make room.

* en/removing-untracked-fixes:
  Documentation: call out commands that nuke untracked files/directories
  Comment important codepaths regarding nuking untracked files/dirs
  unpack-trees: avoid nuking untracked dir in way of locally deleted file
  unpack-trees: avoid nuking untracked dir in way of unmerged file
  Change unpack_trees' 'reset' flag into an enum
  Remove ignored files by default when they are in the way
  unpack-trees: make dir an internal-only struct
  unpack-trees: introduce preserve_ignored to unpack_trees_options
  read-tree, merge-recursive: overwrite ignored files by default
  checkout, read-tree: fix leak of unpack_trees_options.dir
  t2500: add various tests for nuking untracked files

23 files changed, 366 insertions, 74 deletions

diff --git a/Documentation/git-checkout.txt b/Documentation/git-checkout.txt
index b1a6fe4499..d473c9bf38 100644
--- a/Documentation/git-checkout.txt
+++ b/Documentation/git-checkout.txt
@@ -118,8 +118,9 @@ OPTIONS
 -f::
 --force::
 	When switching branches, proceed even if the index or the
-	working tree differs from `HEAD`.  This is used to throw away
-	local changes.
+	working tree differs from `HEAD`, and even if there are untracked
+	files in the way.  This is used to throw away local changes and
+	any untracked files or directories that are in the way.
 +
 When checking out paths from the index, do not fail upon unmerged
 entries; instead, unmerged entries are ignored.
diff --git a/Documentation/git-read-tree.txt b/Documentation/git-read-tree.txt
index 5fa8bab64c..8c3aceb832 100644
--- a/Documentation/git-read-tree.txt
+++ b/Documentation/git-read-tree.txt
@@ -10,8 +10,7 @@ SYNOPSIS
 --------
 [verse]
 'git read-tree' [[-m [--trivial] [--aggressive] | --reset | --prefix=<prefix>]
-		[-u [--exclude-per-directory=<gitignore>] | -i]]
-		[--index-output=<file>] [--no-sparse-checkout]
+		[-u | -i]] [--index-output=<file>] [--no-sparse-checkout]
 		(--empty | <tree-ish1> [<tree-ish2> [<tree-ish3>]])
 
 
@@ -39,8 +38,9 @@ OPTIONS
 
 --reset::
 	Same as -m, except that unmerged entries are discarded instead
-	of failing. When used with `-u`, updates leading to loss of
-	working tree changes will not abort the operation.
+	of failing.  When used with `-u`, updates leading to loss of
+	working tree changes or untracked files or directories will not
+	abort the operation.
 
 -u::
 	After a successful merge, update the files in the work
@@ -88,21 +88,6 @@ OPTIONS
 	The command will refuse to overwrite entries that already
 	existed in the original index file.
 
---exclude-per-directory=<gitignore>::
-	When running the command with `-u` and `-m` options, the
-	merge result may need to overwrite paths that are not
-	tracked in the current branch.  The command usually
-	refuses to proceed with the merge to avoid losing such a
-	path.  However this safety valve sometimes gets in the
-	way.  For example, it often happens that the other
-	branch added a file that used to be a generated file in
-	your branch, and the safety valve triggers when you try
-	to switch to that branch after you ran `make` but before
-	running `make clean` to remove the generated file.  This
-	option tells the command to read per-directory exclude
-	file (usually '.gitignore') and allows such an untracked
-	but explicitly ignored file to be overwritten.
-
 --index-output=<file>::
 	Instead of writing the results out to `$GIT_INDEX_FILE`,
 	write the resulting index in the named file.  While the
diff --git a/Documentation/git-reset.txt b/Documentation/git-reset.txt
index 252e2d4e47..6f7685f53d 100644
--- a/Documentation/git-reset.txt
+++ b/Documentation/git-reset.txt
@@ -69,7 +69,8 @@ linkgit:git-add[1]).
 
 --hard::
 	Resets the index and working tree. Any changes to tracked files in the
-	working tree since `<commit>` are discarded.
+	working tree since `<commit>` are discarded.  Any untracked files or
+	directories in the way of writing any tracked files are simply deleted.
 
 --merge::
 	Resets the index and updates the files in the working tree that are
diff --git a/builtin/am.c b/builtin/am.c
index e4a0ff9cd7..f296226e95 100644
--- a/builtin/am.c
+++ b/builtin/am.c
@@ -1917,7 +1917,8 @@ static int fast_forward_to(struct tree *head, struct tree *remote, int reset)
 	opts.dst_index = &the_index;
 	opts.update = 1;
 	opts.merge = 1;
-	opts.reset = reset;
+	opts.reset = reset ? UNPACK_RESET_PROTECT_UNTRACKED : 0;
+	opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 	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 8c69dcdf72..cbf73b8c9f 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -646,7 +646,9 @@ static int reset_tree(struct tree *tree, const struct checkout_opts *o,
 	opts.head_idx = -1;
 	opts.update = worktree;
 	opts.skip_unmerged = !worktree;
-	opts.reset = 1;
+	opts.reset = o->force ? UNPACK_RESET_OVERWRITE_UNTRACKED :
+				UNPACK_RESET_PROTECT_UNTRACKED;
+	opts.preserve_ignored = (!o->force && !o->overwrite_ignore);
 	opts.merge = 1;
 	opts.fn = oneway_merge;
 	opts.verbose_update = o->show_progress;
@@ -746,11 +748,7 @@ 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);
diff --git a/builtin/clone.c b/builtin/clone.c
index c9d4ca2664..559acf9e03 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -687,6 +687,7 @@ static int checkout(int submodule_progress)
 	opts.update = 1;
 	opts.merge = 1;
 	opts.clone = 1;
+	opts.preserve_ignored = 0;
 	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 3fbdacc7db..0ccd5e1ac8 100644
--- a/builtin/merge.c
+++ b/builtin/merge.c
@@ -680,6 +680,7 @@ 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;
+	opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 	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 485e7b0479..2109c4c9e5 100644
--- a/builtin/read-tree.c
+++ b/builtin/read-tree.c
@@ -38,7 +38,7 @@ static int list_tree(struct object_id *oid)
 }
 
 static const char * const read_tree_usage[] = {
-	N_("git read-tree [(-m [--trivial] [--aggressive] | --reset | --prefix=<prefix>) [-u [--exclude-per-directory=<gitignore>] | -i]] [--no-sparse-checkout] [--index-output=<file>] (--empty | <tree-ish1> [<tree-ish2> [<tree-ish3>]])"),
+	N_("git read-tree [(-m [--trivial] [--aggressive] | --reset | --prefix=<prefix>) [-u | -i]] [--no-sparse-checkout] [--index-output=<file>] (--empty | <tree-ish1> [<tree-ish2> [<tree-ish3>]])"),
 	NULL
 };
 
@@ -53,24 +53,16 @@ static int index_output_cb(const struct option *opt, const char *arg,
 static int exclude_per_directory_cb(const struct option *opt, const char *arg,
 				    int unset)
 {
-	struct dir_struct *dir;
 	struct unpack_trees_options *opts;
 
 	BUG_ON_OPT_NEG(unset);
 
 	opts = (struct unpack_trees_options *)opt->value;
 
-	if (opts->dir)
-		die("more than one --exclude-per-directory given.");
-
-	dir = xcalloc(1, sizeof(*opts->dir));
-	dir->flags |= DIR_SHOW_IGNORED;
-	dir->exclude_per_dir = arg;
-	opts->dir = dir;
-	/* We do not need to nor want to do read-directory
-	 * here; we are merely interested in reusing the
-	 * per directory ignore stack mechanism.
-	 */
+	if (!opts->update)
+		die("--exclude-per-directory is meaningless unless -u");
+	if (strcmp(arg, ".gitignore"))
+		die("--exclude-per-directory argument must be .gitignore");
 	return 0;
 }
 
@@ -174,6 +166,9 @@ int cmd_read_tree(int argc, const char **argv, const char *cmd_prefix)
 	if (1 < opts.merge + opts.reset + prefix_set)
 		die("Which one? -m, --reset, or --prefix?");
 
+	if (opts.reset)
+		opts.reset = UNPACK_RESET_OVERWRITE_UNTRACKED;
+
 	/*
 	 * NEEDSWORK
 	 *
@@ -209,8 +204,9 @@ 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.dir && !opts.update))
-		die("--exclude-per-directory is meaningless unless -u");
+	if (opts.update && !opts.reset)
+		opts.preserve_ignored = 0;
+	/* otherwise, opts.preserve_ignored is irrelevant */
 	if (opts.merge && !opts.index_only)
 		setup_work_tree();
 
diff --git a/builtin/reset.c b/builtin/reset.c
index 51c9e2f43f..7393595349 100644
--- a/builtin/reset.c
+++ b/builtin/reset.c
@@ -67,12 +67,18 @@ static int reset_index(const char *ref, const struct object_id *oid, int reset_t
 	case KEEP:
 	case MERGE:
 		opts.update = 1;
+		opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 		break;
 	case HARD:
 		opts.update = 1;
-		/* fallthrough */
+		opts.reset = UNPACK_RESET_OVERWRITE_UNTRACKED;
+		break;
+	case MIXED:
+		opts.reset = UNPACK_RESET_PROTECT_UNTRACKED;
+		/* but opts.update=0, so working tree not updated */
+		break;
 	default:
-		opts.reset = 1;
+		BUG("invalid reset_type passed to reset_index");
 	}
 
 	read_cache_unmerged();
diff --git a/builtin/stash.c b/builtin/stash.c
index 5512f4942c..cc93ace422 100644
--- a/builtin/stash.c
+++ b/builtin/stash.c
@@ -256,8 +256,10 @@ static int reset_tree(struct object_id *i_tree, int update, int reset)
 	opts.src_index = &the_index;
 	opts.dst_index = &the_index;
 	opts.merge = 1;
-	opts.reset = reset;
+	opts.reset = reset ? UNPACK_RESET_PROTECT_UNTRACKED : 0;
 	opts.update = update;
+	if (update)
+		opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 	opts.fn = oneway_merge;
 
 	if (unpack_trees(nr_trees, t, &opts))
@@ -1533,6 +1535,7 @@ static int do_push_stash(const struct pathspec *ps, const char *stash_msg, int q
 		} else {
 			struct child_process cp = CHILD_PROCESS_INIT;
 			cp.git_cmd = 1;
+			/* BUG: this nukes untracked files in the way */
 			strvec_pushl(&cp.args, "reset", "--hard", "-q",
 				     "--no-recurse-submodules", NULL);
 			if (run_command(&cp)) {
diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index d574d650af..6298cbdd4e 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -3086,6 +3086,10 @@ static int add_submodule(const struct add_data *add_data)
 		prepare_submodule_repo_env(&cp.env_array);
 		cp.git_cmd = 1;
 		cp.dir = add_data->sm_path;
+		/*
+		 * NOTE: we only get here if add_data->force is true, so
+		 * passing --force to checkout is reasonable.
+		 */
 		strvec_pushl(&cp.args, "checkout", "-f", "-q", NULL);
 
 		if (add_data->branch) {
diff --git a/contrib/rerere-train.sh b/contrib/rerere-train.sh
index eeee45dd34..75125d6ae0 100755
--- a/contrib/rerere-train.sh
+++ b/contrib/rerere-train.sh
@@ -91,7 +91,7 @@ do
 		git checkout -q $commit -- .
 		git rerere
 	fi
-	git reset -q --hard
+	git reset -q --hard  # Might nuke untracked files...
 done
 
 if test -z "$branch"
diff --git a/merge-ort.c b/merge-ort.c
index ab42c5d847..e5456f4722 100644
--- a/merge-ort.c
+++ b/merge-ort.c
@@ -4062,11 +4062,7 @@ 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);
@@ -4074,8 +4070,6 @@ 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 5a2d8a60c0..c553751889 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -409,8 +409,11 @@ static int unpack_trees_start(struct merge_options *opt,
 	memset(&opt->priv->unpack_opts, 0, sizeof(opt->priv->unpack_opts));
 	if (opt->priv->call_depth)
 		opt->priv->unpack_opts.index_only = 1;
-	else
+	else {
 		opt->priv->unpack_opts.update = 1;
+		/* FIXME: should only do this if !overwrite_ignore */
+		opt->priv->unpack_opts.preserve_ignored = 0;
+	}
 	opt->priv->unpack_opts.merge = 1;
 	opt->priv->unpack_opts.head_idx = 2;
 	opt->priv->unpack_opts.fn = threeway_merge;
diff --git a/merge.c b/merge.c
index 6e736881d9..2382ff66d3 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 79310ae071..f214df3d96 100644
--- a/reset.c
+++ b/reset.c
@@ -56,9 +56,10 @@ 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;
+	unpack_tree_opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 	init_checkout_metadata(&unpack_tree_opts.meta, switch_to_branch, oid, NULL);
 	if (!detach_head)
-		unpack_tree_opts.reset = 1;
+		unpack_tree_opts.reset = UNPACK_RESET_PROTECT_UNTRACKED;
 
 	if (repo_read_index_unmerged(r) < 0) {
 		ret = error(_("could not read index"));
diff --git a/sequencer.c b/sequencer.c
index 64b1f2e681..b92dae1216 100644
--- a/sequencer.c
+++ b/sequencer.c
@@ -3693,6 +3693,7 @@ static int do_reset(struct repository *r,
 	unpack_tree_opts.fn = oneway_merge;
 	unpack_tree_opts.merge = 1;
 	unpack_tree_opts.update = 1;
+	unpack_tree_opts.preserve_ignored = 0; /* FIXME: !overwrite_ignore */
 	init_checkout_metadata(&unpack_tree_opts.meta, name, &oid, NULL);
 
 	if (repo_read_index_unmerged(r)) {
diff --git a/submodule.c b/submodule.c
index 96487517f9..f3c99634a9 100644
--- a/submodule.c
+++ b/submodule.c
@@ -1896,6 +1896,7 @@ static void submodule_reset_index(const char *path)
 
 	strvec_pushf(&cp.args, "--super-prefix=%s%s/",
 		     get_super_prefix_or_empty(), path);
+	/* TODO: determine if this might overwright untracked files */
 	strvec_pushl(&cp.args, "read-tree", "-u", "--reset", NULL);
 
 	strvec_push(&cp.args, empty_tree_oid_hex());
diff --git a/t/t1013-read-tree-submodule.sh b/t/t1013-read-tree-submodule.sh
index b6df7444c0..bfc90d4cf2 100755
--- a/t/t1013-read-tree-submodule.sh
+++ b/t/t1013-read-tree-submodule.sh
@@ -6,7 +6,6 @@ test_description='read-tree can handle submodules'
 . "$TEST_DIRECTORY"/lib-submodule-update.sh
 
 KNOWN_FAILURE_DIRECTORY_SUBMODULE_CONFLICTS=1
-KNOWN_FAILURE_SUBMODULE_OVERWRITE_IGNORED_UNTRACKED=1
 
 test_submodule_switch_recursing_with_args "read-tree -u -m"
 
diff --git a/t/t2500-untracked-overwriting.sh b/t/t2500-untracked-overwriting.sh
new file mode 100755
index 0000000000..5c0bf4d21f
--- /dev/null
+++ b/t/t2500-untracked-overwriting.sh
@@ -0,0 +1,244 @@
+#!/bin/sh
+
+test_description='Test handling of overwriting untracked files'
+
+. ./test-lib.sh
+
+test_setup_reset () {
+	git init reset_$1 &&
+	(
+		cd reset_$1 &&
+		test_commit init &&
+
+		git branch stable &&
+		git branch work &&
+
+		git checkout work &&
+		test_commit foo &&
+
+		git checkout stable
+	)
+}
+
+test_expect_success 'reset --hard will nuke untracked files/dirs' '
+	test_setup_reset hard &&
+	(
+		cd reset_hard &&
+		git ls-tree -r stable &&
+		git log --all --name-status --oneline &&
+		git ls-tree -r work &&
+
+		mkdir foo.t &&
+		echo precious >foo.t/file &&
+		echo foo >expect &&
+
+		git reset --hard work &&
+
+		# check that untracked directory foo.t/ was nuked
+		test_path_is_file foo.t &&
+		test_cmp expect foo.t
+	)
+'
+
+test_expect_success 'reset --merge will preserve untracked files/dirs' '
+	test_setup_reset merge &&
+	(
+		cd reset_merge &&
+
+		mkdir foo.t &&
+		echo precious >foo.t/file &&
+		cp foo.t/file expect &&
+
+		test_must_fail git reset --merge work 2>error &&
+		test_cmp expect foo.t/file &&
+		grep "Updating .foo.t. would lose untracked files" error
+	)
+'
+
+test_expect_success 'reset --keep will preserve untracked files/dirs' '
+	test_setup_reset keep &&
+	(
+		cd reset_keep &&
+
+		mkdir foo.t &&
+		echo precious >foo.t/file &&
+		cp foo.t/file expect &&
+
+		test_must_fail git reset --merge work 2>error &&
+		test_cmp expect foo.t/file &&
+		grep "Updating.*foo.t.*would lose untracked files" error
+	)
+'
+
+test_setup_checkout_m () {
+	git init checkout &&
+	(
+		cd checkout &&
+		test_commit init &&
+
+		test_write_lines file has some >filler &&
+		git add filler &&
+		git commit -m filler &&
+
+		git branch stable &&
+
+		git switch -c work &&
+		echo stuff >notes.txt &&
+		test_write_lines file has some words >filler &&
+		git add notes.txt filler &&
+		git commit -m filler &&
+
+		git checkout stable
+	)
+}
+
+test_expect_success 'checkout -m does not nuke untracked file' '
+	test_setup_checkout_m &&
+	(
+		cd checkout &&
+
+		# Tweak filler
+		test_write_lines this file has some >filler &&
+		# Make an untracked file, save its contents in "expect"
+		echo precious >notes.txt &&
+		cp notes.txt expect &&
+
+		test_must_fail git checkout -m work &&
+		test_cmp expect notes.txt
+	)
+'
+
+test_setup_sequencing () {
+	git init sequencing_$1 &&
+	(
+		cd sequencing_$1 &&
+		test_commit init &&
+
+		test_write_lines this file has some words >filler &&
+		git add filler &&
+		git commit -m filler &&
+
+		mkdir -p foo/bar &&
+		test_commit foo/bar/baz &&
+
+		git branch simple &&
+		git branch fooey &&
+
+		git checkout fooey &&
+		git rm foo/bar/baz.t &&
+		echo stuff >>filler &&
+		git add -u &&
+		git commit -m "changes" &&
+
+		git checkout simple &&
+		echo items >>filler &&
+		echo newstuff >>newfile &&
+		git add filler newfile &&
+		git commit -m another
+	)
+}
+
+test_expect_success 'git rebase --abort and untracked files' '
+	test_setup_sequencing rebase_abort_and_untracked &&
+	(
+		cd sequencing_rebase_abort_and_untracked &&
+		git checkout fooey &&
+		test_must_fail git rebase simple &&
+
+		cat init.t &&
+		git rm init.t &&
+		echo precious >init.t &&
+		cp init.t expect &&
+		git status --porcelain &&
+		test_must_fail git rebase --abort &&
+		test_cmp expect init.t
+	)
+'
+
+test_expect_success 'git rebase fast forwarding and untracked files' '
+	test_setup_sequencing rebase_fast_forward_and_untracked &&
+	(
+		cd sequencing_rebase_fast_forward_and_untracked &&
+		git checkout init &&
+		echo precious >filler &&
+		cp filler expect &&
+		test_must_fail git rebase init simple &&
+		test_cmp expect filler
+	)
+'
+
+test_expect_failure 'git rebase --autostash and untracked files' '
+	test_setup_sequencing rebase_autostash_and_untracked &&
+	(
+		cd sequencing_rebase_autostash_and_untracked &&
+		git checkout simple &&
+		git rm filler &&
+		mkdir filler &&
+		echo precious >filler/file &&
+		cp filler/file expect &&
+		git rebase --autostash init &&
+		test_path_is_file filler/file
+	)
+'
+
+test_expect_failure 'git stash and untracked files' '
+	test_setup_sequencing stash_and_untracked_files &&
+	(
+		cd sequencing_stash_and_untracked_files &&
+		git checkout simple &&
+		git rm filler &&
+		mkdir filler &&
+		echo precious >filler/file &&
+		cp filler/file expect &&
+		git status --porcelain &&
+		git stash push &&
+		git status --porcelain &&
+		test_path_is_file filler/file
+	)
+'
+
+test_expect_success 'git am --abort and untracked dir vs. unmerged file' '
+	test_setup_sequencing am_abort_and_untracked &&
+	(
+		cd sequencing_am_abort_and_untracked &&
+		git format-patch -1 --stdout fooey >changes.mbox &&
+		test_must_fail git am --3way changes.mbox &&
+
+		# Delete the conflicted file; we will stage and commit it later
+		rm filler &&
+
+		# Put an unrelated untracked directory there
+		mkdir filler &&
+		echo foo >filler/file1 &&
+		echo bar >filler/file2 &&
+
+		test_must_fail git am --abort 2>errors &&
+		test_path_is_dir filler &&
+		grep "Updating .filler. would lose untracked files in it" errors
+	)
+'
+
+test_expect_success 'git am --skip and untracked dir vs deleted file' '
+	test_setup_sequencing am_skip_and_untracked &&
+	(
+		cd sequencing_am_skip_and_untracked &&
+		git checkout fooey &&
+		git format-patch -1 --stdout simple >changes.mbox &&
+		test_must_fail git am --3way changes.mbox &&
+
+		# Delete newfile
+		rm newfile &&
+
+		# Put an unrelated untracked directory there
+		mkdir newfile &&
+		echo foo >newfile/file1 &&
+		echo bar >newfile/file2 &&
+
+		# Change our mind about resolutions, just skip this patch
+		test_must_fail git am --skip 2>errors &&
+		test_path_is_dir newfile &&
+		grep "Updating .newfile. would lose untracked files in it" errors
+	)
+'
+
+test_done
diff --git a/t/t7112-reset-submodule.sh b/t/t7112-reset-submodule.sh
index 19830d9036..a3e2413bc3 100755
--- a/t/t7112-reset-submodule.sh
+++ b/t/t7112-reset-submodule.sh
@@ -6,7 +6,6 @@ test_description='reset can handle submodules'
 . "$TEST_DIRECTORY"/lib-submodule-update.sh
 
 KNOWN_FAILURE_DIRECTORY_SUBMODULE_CONFLICTS=1
-KNOWN_FAILURE_SUBMODULE_OVERWRITE_IGNORED_UNTRACKED=1
 
 test_submodule_switch_recursing_with_args "reset --keep"
 
diff --git a/unpack-trees.c b/unpack-trees.c
index 8ea0a542da..a7e1712d23 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -1694,9 +1694,15 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 	static struct cache_entry *dfc;
 	struct pattern_list pl;
 	int free_pattern_list = 0;
+	struct dir_struct dir = DIR_INIT;
+
+	if (o->reset == UNPACK_RESET_INVALID)
+		BUG("o->reset had a value of 1; should be UNPACK_TREES_*_UNTRACKED");
 
 	if (len > MAX_UNPACK_TREES)
 		die("unpack_trees takes at most %d trees", MAX_UNPACK_TREES);
+	if (o->dir)
+		BUG("o->dir is for internal use only");
 
 	trace_performance_enter();
 	trace2_region_enter("unpack_trees", "unpack_trees", the_repository);
@@ -1707,6 +1713,16 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 		ensure_full_index(o->dst_index);
 	}
 
+	if (o->reset == UNPACK_RESET_OVERWRITE_UNTRACKED &&
+	    o->preserve_ignored)
+		BUG("UNPACK_RESET_OVERWRITE_UNTRACKED incompatible with preserved ignored files");
+
+	if (!o->preserve_ignored) {
+		o->dir = &dir;
+		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 +1884,10 @@ 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);
+		o->dir = NULL;
+	}
 	trace2_region_leave("unpack_trees", "unpack_trees", the_repository);
 	trace_performance_leave("unpack_trees");
 	return ret;
@@ -2158,9 +2178,15 @@ static int icase_exists(struct unpack_trees_options *o, const char *name, int le
 	return src && !ie_match_stat(o->src_index, src, st, CE_MATCH_IGNORE_VALID|CE_MATCH_IGNORE_SKIP_WORKTREE);
 }
 
+enum absent_checking_type {
+	COMPLETELY_ABSENT,
+	ABSENT_ANY_DIRECTORY
+};
+
 static int check_ok_to_remove(const char *name, int len, int dtype,
 			      const struct cache_entry *ce, struct stat *st,
 			      enum unpack_trees_error_types error_type,
+			      enum absent_checking_type absent_type,
 			      struct unpack_trees_options *o)
 {
 	const struct cache_entry *result;
@@ -2195,6 +2221,10 @@ static int check_ok_to_remove(const char *name, int len, int dtype,
 		return 0;
 	}
 
+	/* If we only care about directories, then we can remove */
+	if (absent_type == ABSENT_ANY_DIRECTORY)
+		return 0;
+
 	/*
 	 * The previous round may already have decided to
 	 * delete this path, which is in a subdirectory that
@@ -2215,12 +2245,14 @@ static int check_ok_to_remove(const char *name, int len, int dtype,
  */
 static int verify_absent_1(const struct cache_entry *ce,
 			   enum unpack_trees_error_types error_type,
+			   enum absent_checking_type absent_type,
 			   struct unpack_trees_options *o)
 {
 	int len;
 	struct stat st;
 
-	if (o->index_only || o->reset || !o->update)
+	if (o->index_only || !o->update ||
+	    o->reset == UNPACK_RESET_OVERWRITE_UNTRACKED)
 		return 0;
 
 	len = check_leading_path(ce->name, ce_namelen(ce), 0);
@@ -2240,7 +2272,8 @@ static int verify_absent_1(const struct cache_entry *ce,
 								NULL, o);
 			else
 				ret = check_ok_to_remove(path, len, DT_UNKNOWN, NULL,
-							 &st, error_type, o);
+							 &st, error_type,
+							 absent_type, o);
 		}
 		free(path);
 		return ret;
@@ -2255,7 +2288,7 @@ static int verify_absent_1(const struct cache_entry *ce,
 
 		return check_ok_to_remove(ce->name, ce_namelen(ce),
 					  ce_to_dtype(ce), ce, &st,
-					  error_type, o);
+					  error_type, absent_type, o);
 	}
 }
 
@@ -2265,14 +2298,23 @@ static int verify_absent(const struct cache_entry *ce,
 {
 	if (!o->skip_sparse_checkout && (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
 		return 0;
-	return verify_absent_1(ce, error_type, o);
+	return verify_absent_1(ce, error_type, COMPLETELY_ABSENT, o);
+}
+
+static int verify_absent_if_directory(const struct cache_entry *ce,
+				      enum unpack_trees_error_types error_type,
+				      struct unpack_trees_options *o)
+{
+	if (!o->skip_sparse_checkout && (ce->ce_flags & CE_NEW_SKIP_WORKTREE))
+		return 0;
+	return verify_absent_1(ce, error_type, ABSENT_ANY_DIRECTORY, o);
 }
 
 static int verify_absent_sparse(const struct cache_entry *ce,
 				enum unpack_trees_error_types error_type,
 				struct unpack_trees_options *o)
 {
-	return verify_absent_1(ce, error_type, o);
+	return verify_absent_1(ce, error_type, COMPLETELY_ABSENT, o);
 }
 
 static int merged_entry(const struct cache_entry *ce,
@@ -2346,6 +2388,12 @@ static int merged_entry(const struct cache_entry *ce,
 		 * Previously unmerged entry left as an existence
 		 * marker by read_index_unmerged();
 		 */
+		if (verify_absent_if_directory(merge,
+				  ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN, o)) {
+			discard_cache_entry(merge);
+			return -1;
+		}
+
 		invalidate_ce_path(old, o);
 	}
 
@@ -2363,7 +2411,10 @@ static int deleted_entry(const struct cache_entry *ce,
 		if (verify_absent(ce, ERROR_WOULD_LOSE_UNTRACKED_REMOVED, o))
 			return -1;
 		return 0;
+	} else if (verify_absent_if_directory(ce, ERROR_WOULD_LOSE_UNTRACKED_REMOVED, o)) {
+		return -1;
 	}
+
 	if (!(old->ce_flags & CE_CONFLICTED) && verify_uptodate(old, o))
 		return -1;
 	add_entry(o, ce, CE_REMOVE, 0);
diff --git a/unpack-trees.h b/unpack-trees.h
index 2d88b19dca..71ffb7eeb0 100644
--- a/unpack-trees.h
+++ b/unpack-trees.h
@@ -45,10 +45,17 @@ void setup_unpack_trees_porcelain(struct unpack_trees_options *opts,
  */
 void clear_unpack_trees_porcelain(struct unpack_trees_options *opts);
 
+enum unpack_trees_reset_type {
+	UNPACK_RESET_NONE = 0,    /* traditional "false" value; still valid */
+	UNPACK_RESET_INVALID = 1, /* "true" no longer valid; use below values */
+	UNPACK_RESET_PROTECT_UNTRACKED,
+	UNPACK_RESET_OVERWRITE_UNTRACKED
+};
+
 struct unpack_trees_options {
-	unsigned int reset,
-		     merge,
+	unsigned int merge,
 		     update,
+		     preserve_ignored,
 		     clone,
 		     index_only,
 		     nontrivial_merge,
@@ -64,9 +71,9 @@ struct unpack_trees_options {
 		     exiting_early,
 		     show_all_errors,
 		     dry_run;
+	enum unpack_trees_reset_type reset;
 	const char *prefix;
 	int cache_bottom;
-	struct dir_struct *dir;
 	struct pathspec *pathspec;
 	merge_fn_t fn;
 	const char *msgs[NB_UNPACK_TREES_WARNING_TYPES];
@@ -88,6 +95,7 @@ struct unpack_trees_options {
 	struct index_state result;
 
 	struct pattern_list *pl; /* for internal use */
+	struct dir_struct *dir; /* for internal use only */
 	struct checkout_metadata meta;
 };