diff --git a/dvc/repo/checkout.py b/dvc/repo/checkout.py
index 51c3dc5f7a5..65a3fb96c2f 100644
--- a/dvc/repo/checkout.py
+++ b/dvc/repo/checkout.py
@@ -30,35 +30,6 @@ def _remove_unused_links(repo):
     return ret
 
 
-def get_all_files_numbers(pairs):
-    return sum(stage.get_all_files_number(filter_info) for stage, filter_info in pairs)
-
-
-def _collect_pairs(
-    self: "Repo", targets, with_deps: bool, recursive: bool
-) -> Set["StageInfo"]:
-    from dvc.stage.exceptions import StageFileBadNameError, StageFileDoesNotExistError
-
-    pairs: Set["StageInfo"] = set()
-    for target in targets:
-        try:
-            pairs.update(
-                self.stage.collect_granular(
-                    target, with_deps=with_deps, recursive=recursive
-                )
-            )
-        except (
-            StageFileDoesNotExistError,
-            StageFileBadNameError,
-            NoOutputOrStageError,
-        ) as exc:
-            if not target:
-                raise
-            raise CheckoutErrorSuggestGit(target) from exc
-
-    return pairs
-
-
 @locked
 def checkout(
     self,
@@ -70,13 +41,18 @@ def checkout(
     allow_missing=False,
     **kwargs,
 ):
+    from dvc import prompt
     from dvc.fs.callbacks import Callback
+    from dvc.repo.index import build_data_index
+    from dvc.stage.exceptions import StageFileBadNameError, StageFileDoesNotExistError
+    from dvc_data.index.checkout import ADD, DELETE, MODIFY
+    from dvc_data.index.checkout import checkout as icheckout
+    from dvc_data.index.diff import diff as idiff
 
     stats: Dict[str, List[str]] = {
         "added": [],
         "deleted": [],
         "modified": [],
-        "failed": [],
     }
     if not targets:
         targets = [None]
@@ -85,28 +61,76 @@ def checkout(
     if isinstance(targets, str):
         targets = [targets]
 
-    pairs = _collect_pairs(self, targets, with_deps, recursive)
-    total = get_all_files_numbers(pairs)
+    def onerror(target, exc):
+        if target and isinstance(
+            exc,
+            (
+                StageFileDoesNotExistError,
+                StageFileBadNameError,
+                NoOutputOrStageError,
+            ),
+        ):
+            raise CheckoutErrorSuggestGit(target) from exc
+        raise
+
+    view = self.index.targets_view(
+        targets,
+        recursive=recursive,
+        with_deps=with_deps,
+        onerror=onerror,
+    )
+
+    old = build_data_index(view, self.root_dir, self.fs, compute_hash=True)
+    new = view.data["repo"]
+
+    total = len(new)
     with Callback.as_tqdm_callback(
         unit="file",
         desc="Checkout",
         disable=total == 0,
     ) as cb:
-        cb.set_size(total)
-        for stage, filter_info in pairs:
-            result = stage.checkout(
-                force=force,
-                progress_callback=cb,
-                relink=relink,
-                filter_info=filter_info,
-                allow_missing=allow_missing,
-                **kwargs,
-            )
-            for key, items in result.items():
-                stats[key].extend(_fspath_dir(path) for path in items)
-
-    if stats.get("failed"):
-        raise CheckoutError(stats["failed"], stats)
-
-    del stats["failed"]
+        changes = icheckout(
+            new,
+            self.root_dir,
+            self.fs,
+            old=old,
+            callback=cb,
+            hash_only=True,
+            delete=True,
+            prompt=prompt.confirm,
+            update_meta=False,
+            relink=relink,
+            force=force,
+            **kwargs,
+        )
+
+    def _adapt_path(entry):
+        parts = list(entry.key)
+        if entry.meta and entry.meta.isdir:
+            parts.append("")
+        return self.fs.path.join(*parts)
+
+    stats["added"].extend(_adapt_path(change.new) for change in changes[ADD])
+    stats["deleted"].extend(_adapt_path(change.old) for change in changes[DELETE])
+    stats["modified"].extend(_adapt_path(change.new) for change in changes[MODIFY])
+
+    from itertools import chain
+
+    top_keys = {key for key, _ in new.iteritems(shallow=True)}
+    changed_keys = {
+        change.key for change in chain(changes[ADD], changes[DELETE], changes[MODIFY])
+    }
+    for key in top_keys:
+        for changed_key in changed_keys:
+            if len(changed_key) >= len(key) and changed_key[: len(key)] == key:
+                self.state.save_link(self.fs.path.join(self.root_dir, *key), self.fs)
+
+    failed = [
+        entry
+        for _, entry in new.iteritems()
+        if not entry.hash_info and not (entry.meta and entry.meta.isdir)
+    ]
+    if failed:
+        raise CheckoutError([_adapt_path(entry) for entry in failed], stats)
+
     return stats
diff --git a/dvc/repo/index.py b/dvc/repo/index.py
index 1a3227c991c..dbf89d0bd33 100644
--- a/dvc/repo/index.py
+++ b/dvc/repo/index.py
@@ -534,6 +534,8 @@ def _data_prefixes(self) -> Dict[str, "_DataPrefixes"]:
             lambda: _DataPrefixes(set(), set())
         )
         for out, filter_info in self._filtered_outs:
+            if not out.use_cache:
+                continue
             workspace, key = out.index_key
             if filter_info and out.fs.path.isin(filter_info, out.fs_path):
                 key = key + out.fs.path.relparts(filter_info, out.fs_path)
@@ -550,6 +552,9 @@ def data_keys(self) -> Dict[str, Set["DataIndexKey"]]:
         ret: Dict[str, Set["DataIndexKey"]] = defaultdict(set)
 
         for out, filter_info in self._filtered_outs:
+            if not out.use_cache:
+                continue
+
             workspace, key = out.index_key
             if filter_info and out.fs.path.isin(filter_info, out.fs_path):
                 key = key + out.fs.path.relparts(filter_info, out.fs_path)
diff --git a/dvc/stage/__init__.py b/dvc/stage/__init__.py
index 1f003678455..b7e8d6e1083 100644
--- a/dvc/stage/__init__.py
+++ b/dvc/stage/__init__.py
@@ -728,11 +728,6 @@ def outs_cached(self) -> bool:
             for out in self.outs
         )
 
-    def get_all_files_number(self, filter_info=None) -> int:
-        return sum(
-            out.get_files_number(filter_info) for out in self.filter_outs(filter_info)
-        )
-
     def get_used_objs(
         self, *args, **kwargs
     ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
diff --git a/tests/func/test_checkout.py b/tests/func/test_checkout.py
index d308b633fc3..c1957df2a2d 100644
--- a/tests/func/test_checkout.py
+++ b/tests/func/test_checkout.py
@@ -294,19 +294,6 @@ def test_checkout_directory(tmp_dir, dvc):
     assert os.path.exists("data")
 
 
-def test_checkout_hook(mocker, tmp_dir, dvc):
-    """Test that dvc checkout handles EOFError gracefully, which is what
-    it will experience when running in a git hook.
-    """
-    tmp_dir.dvc_gen({"data": {"foo": "foo"}})
-    mocker.patch("sys.stdout.isatty", return_value=True)
-    mocker.patch("dvc.prompt.input", side_effect=EOFError)
-
-    (tmp_dir / "data").gen("test", "test")
-    with pytest.raises(ConfirmRemoveError):
-        dvc.checkout()
-
-
 def test_checkout_suggest_git(tmp_dir, dvc, scm):
     with pytest.raises(CheckoutErrorSuggestGit) as e:
         dvc.checkout(targets="gitbranch")
@@ -432,7 +419,7 @@ def test_partial_checkout(tmp_dir, dvc, target):
     tmp_dir.dvc_gen({"dir": {"subdir": {"file": "file"}, "other": "other"}})
     shutil.rmtree("dir")
     stats = dvc.checkout([target])
-    assert stats["added"] == ["dir" + os.sep]
+    assert set(stats["added"]) == {"dir" + os.sep, os.path.join("dir", "subdir", "file")}
     assert list(walk_files("dir")) == [os.path.join("dir", "subdir", "file")]
 
 
@@ -463,7 +450,13 @@ def test_stats_on_checkout(tmp_dir, dvc, scm):
 
     scm.checkout("-")
     stats = dvc.checkout()
-    assert set(stats["added"]) == {"bar", "dir" + os.sep, "foo"}
+    assert set(stats["added"]) == {
+        "bar",
+        "dir" + os.sep,
+        os.path.join("dir", "subdir", "file"),
+        os.path.join("dir", "other"),
+        "foo",
+    }
 
     tmp_dir.gen({"lorem": "lorem", "bar": "new bar", "dir2": {"file": "file"}})
     (tmp_dir / "foo").unlink()
@@ -479,7 +472,11 @@ def test_stats_on_checkout(tmp_dir, dvc, scm):
     scm.checkout("-")
     stats = dvc.checkout()
     assert set(stats["modified"]) == {"bar"}
-    assert set(stats["added"]) == {"dir2" + os.sep, "lorem"}
+    assert set(stats["added"]) == {
+        "dir2" + os.sep,
+        os.path.join("dir2", "file"),
+        "lorem",
+    }
     assert set(stats["deleted"]) == {"foo"}
 
 
@@ -518,11 +515,11 @@ def test_stats_on_added_file_from_tracked_dir(tmp_dir, dvc, scm):
     tmp_dir.gen("dir/subdir/newfile", "newfile")
     tmp_dir.dvc_add("dir", commit="add newfile")
     scm.checkout("HEAD~")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep], "deleted": [os.path.join("dir", "subdir", "newfile")]}
     assert dvc.checkout() == empty_checkout
 
     scm.checkout("-")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep], "added": [os.path.join("dir", "subdir", "newfile")]}
     assert dvc.checkout() == empty_checkout
 
 
@@ -535,11 +532,11 @@ def test_stats_on_updated_file_from_tracked_dir(tmp_dir, dvc, scm):
     tmp_dir.gen("dir/subdir/file", "what file?")
     tmp_dir.dvc_add("dir", commit="update file")
     scm.checkout("HEAD~")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep, os.path.join("dir", "subdir", "file")]}
     assert dvc.checkout() == empty_checkout
 
     scm.checkout("-")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep, os.path.join("dir", "subdir", "file")]}
     assert dvc.checkout() == empty_checkout
 
 
@@ -552,11 +549,11 @@ def test_stats_on_removed_file_from_tracked_dir(tmp_dir, dvc, scm):
     (tmp_dir / "dir" / "subdir" / "file").unlink()
     tmp_dir.dvc_add("dir", commit="removed file from subdir")
     scm.checkout("HEAD~")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep], "added": [os.path.join("dir", "subdir", "file")]}
     assert dvc.checkout() == empty_checkout
 
     scm.checkout("-")
-    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep]}
+    assert dvc.checkout() == {**empty_checkout, "modified": ["dir" + os.sep], "deleted": [os.path.join("dir", "subdir", "file")]}
     assert dvc.checkout() == empty_checkout