diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 75d1678..8429cc3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -46,7 +46,7 @@ repos:
         additional_dependencies:
           - flake8-bugbear==23.1.20
           - flake8-comprehensions==3.10.1
-          - flake8-pytest-style==1.6
+          - flake8-pytest-style==1.7
           - flake8-spellcheck==0.28
           - flake8-unused-arguments==0.0.13
           - flake8-noqa==1.3
diff --git a/README.md b/README.md
index f99eacb..b2a3cf6 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ Apply a consistent format to `pyproject.toml` files.
 
 ```yaml
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: "0.6.0"
+  rev: "0.9.0"
   hooks:
     - id: pyproject-fmt
 ```
diff --git a/docs/changelog.rst b/docs/changelog.rst
deleted file mode 100644
index ae241cf..0000000
--- a/docs/changelog.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-changelog
-=========
-
-v0.3.5 (2022-08-12)
--------------------
-* Support ``tomlkit>=0.11`` and CPython 3.11.
-
-v0.3.4 (2022-06-26)
--------------------
-* Fix project links
-
-v0.3.3 (2022-03-23)
--------------------
-* Fix help message referring to tox.ini files
-
-v0.3.2 (2022-03-01)
--------------------
-* Fix invalid newline inside inline-table - by :user:`abravalheri`.
-
-v0.3.1 (2022-02-27)
--------------------
-* Better handling of PEP-508 dependencies by using the ``packaging`` module instead of the our own parsing logic - by
-  :user:`abravalheri`.
-
-v0.3.0 (2022-02-27)
--------------------
-* Handle ``project`` section in first iteration - by :user:`gaborbernat`.
-* Add documentation build to the project - by :user:`gaborbernat`.
-* Add a programmatic API as :meth:`format_pyproject <pyproject_fmt.format_pyproject>` - by :user:`gaborbernat`.
-
-v0.2.0 (2022-02-21)
--------------------
-* Handle ``build-system`` section - by :user:`gaborbernat`.
-
-v0.1.0 (2022-02-21)
--------------------
-* Create base and reserve PyPI name - by :user:`gaborbernat`.
diff --git a/docs/index.rst b/docs/index.rst
index 6be18f6..da6ac3c 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -2,6 +2,7 @@ pyproject-fmt
 =============
 
 Apply a consistent format to your ``pyproject.toml`` file with comment support.
+See `changelog here <https://github.com/tox-dev/pyproject-fmt/releases>`_.
 
 Use
 ---
@@ -24,7 +25,7 @@ See :gh:`pre-commit/pre-commit` for instructions, sample ``.pre-commit-config.ya
 .. code-block:: yaml
 
     - repo: https://github.com/tox-dev/pyproject-fmt
-      rev: "0.4.1"
+      rev: "0.9.0"
       hooks:
         - id: pyproject-fmt
 
@@ -46,4 +47,3 @@ API
    :hidden:
 
    self
-   changelog
diff --git a/pyproject.toml b/pyproject.toml
index dd0d9aa..8aa05be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 build-backend = "hatchling.build"
 requires = [
   "hatch-vcs>=0.3",
-  "hatchling>=1.12.2",
+  "hatchling>=1.13",
 ]
 
 [project]
@@ -39,7 +39,7 @@ optional-dependencies.docs = [
   "furo>=2022.12.7",
   "sphinx>=6.1.3",
   "sphinx-argparse-cli>=1.11",
-  "sphinx-autodoc-typehints!=1.23.4,>1",
+  "sphinx-autodoc-typehints!=1.23.4,>=1.22",
   "sphinx-copybutton>=0.5.1",
 ]
 optional-dependencies.test = [
@@ -51,22 +51,28 @@ optional-dependencies.test = [
 urls."Bug Tracker" = "https://github.com/tox-dev/pyproject-fmt/issues"
 urls.Documentation = "https://github.com/tox-dev/pyproject-fmt/"
 urls."Source Code" = "https://github.com/tox-dev/pyproject-fmt"
+urls."Changelog" = "https://github.com/tox-dev/pyproject-fmt/releases"
 scripts.pyproject-fmt = "pyproject_fmt.__main__:run"
 
-
 [tool.hatch]
 build.dev-mode-dirs = ["src"]
 build.hooks.vcs.version-file = "src/pyproject_fmt/_version.py"
 build.targets.sdist.include = ["/src", "/tests"]
 version.source = "vcs"
 
+[tool.black]
+line-length = 120
+
 [tool.isort]
 known_first_party = ["helpers", "package_info"]
 profile = "black"
 add_imports = ["from __future__ import annotations"]
 
-[tool.black]
-line-length = 120
+[tool.flake8]
+max-line-length = 120
+unused-arguments-ignore-abstract-functions = true
+noqa-require-code = true
+dictionaries = ["en_US", "python", "technical", "django"]
 
 [tool.pytest]
 ini_options.testpaths = ["tests"]
@@ -82,9 +88,3 @@ run.plugins = ["covdefaults"]
 [tool.mypy]
 show_error_codes = true
 strict = true
-
-[tool.flake8]
-max-line-length = 120
-unused-arguments-ignore-abstract-functions = true
-noqa-require-code = true
-dictionaries = ["en_US", "python", "technical", "django"]
diff --git a/src/pyproject_fmt/cli.py b/src/pyproject_fmt/cli.py
index d8abfc7..5e5aada 100644
--- a/src/pyproject_fmt/cli.py
+++ b/src/pyproject_fmt/cli.py
@@ -33,6 +33,8 @@ def pyproject_toml_path_creator(argument: str) -> Path:
     :return: the pyproject.toml path
     """
     path = Path(argument).absolute()
+    if path.is_dir():
+        path = path / "pyproject.toml"
     if not path.exists():
         raise ArgumentTypeError("path does not exist")
     if not path.is_file():
diff --git a/src/pyproject_fmt/formatter/__init__.py b/src/pyproject_fmt/formatter/__init__.py
index f92fb7d..f7d9de5 100644
--- a/src/pyproject_fmt/formatter/__init__.py
+++ b/src/pyproject_fmt/formatter/__init__.py
@@ -6,11 +6,13 @@
 from .build_system import fmt_build_system
 from .config import Config
 from .project import fmt_project
+from .tools import fmt_tools
 
 
 def _perform(parsed: TOMLDocument, conf: Config) -> None:
     fmt_build_system(parsed, conf)
     fmt_project(parsed, conf)
+    fmt_tools(parsed, conf)
 
 
 def format_pyproject(conf: Config) -> str:
diff --git a/src/pyproject_fmt/formatter/build_system.py b/src/pyproject_fmt/formatter/build_system.py
index b570a8b..2d31376 100644
--- a/src/pyproject_fmt/formatter/build_system.py
+++ b/src/pyproject_fmt/formatter/build_system.py
@@ -7,7 +7,7 @@
 
 from .config import Config
 from .pep508 import normalize_pep508_array
-from .util import order_keys, sorted_array
+from .util import ensure_newline_at_end, order_keys, sorted_array
 
 
 def fmt_build_system(parsed: TOMLDocument, conf: Config) -> None:
@@ -16,6 +16,7 @@ def fmt_build_system(parsed: TOMLDocument, conf: Config) -> None:
         normalize_pep508_array(cast(Optional[Array], system.get("requires")), conf.indent)
         sorted_array(cast(Optional[Array], system.get("backend-path")), indent=conf.indent)
         order_keys(system, ("build-backend", "requires", "backend-path"))
+        ensure_newline_at_end(system)
 
 
 __all__ = [
diff --git a/src/pyproject_fmt/formatter/project.py b/src/pyproject_fmt/formatter/project.py
index eb5fabb..bcefd5d 100644
--- a/src/pyproject_fmt/formatter/project.py
+++ b/src/pyproject_fmt/formatter/project.py
@@ -8,7 +8,7 @@
 
 from .config import Config
 from .pep508 import normalize_pep508_array
-from .util import order_keys, sorted_array
+from .util import ensure_newline_at_end, order_keys, sorted_array
 
 
 def fmt_project(parsed: TOMLDocument, conf: Config) -> None:
@@ -56,6 +56,7 @@ def fmt_project(parsed: TOMLDocument, conf: Config) -> None:
     # these go at the end as they may be inline or exploded
     key_order.extend(["optional-dependencies", "urls", "scripts", "gui-scripts", "entry-points"])
     order_keys(project, key_order)
+    ensure_newline_at_end(project)
 
 
 __all__ = [
diff --git a/src/pyproject_fmt/formatter/tools.py b/src/pyproject_fmt/formatter/tools.py
new file mode 100644
index 0000000..5aaacc3
--- /dev/null
+++ b/src/pyproject_fmt/formatter/tools.py
@@ -0,0 +1,35 @@
+from __future__ import annotations
+
+from typing import cast
+
+from tomlkit import TOMLDocument
+from tomlkit.items import Table
+
+from .config import Config
+from .util import ensure_newline_at_end, order_keys
+
+
+def fmt_tools(parsed: TOMLDocument, conf: Config) -> None:  # noqa: U100
+    tools: Table | None = parsed.get("tool")
+    if tools is None:
+        return None
+    for tool in tools:
+        table = tools[tool]
+        ensure_newline_at_end(cast(Table, table))
+    order = [
+        "setuptools",
+        "setuptools_scm",
+        "hatch",
+        "black",
+        "isort",
+        "flake8",
+        "pytest",
+        "coverage",
+        "mypy",
+    ]
+    order_keys(tools, to_pin=order)
+
+
+__all__ = [
+    "fmt_tools",
+]
diff --git a/src/pyproject_fmt/formatter/util.py b/src/pyproject_fmt/formatter/util.py
index f3a81e5..dba1f59 100644
--- a/src/pyproject_fmt/formatter/util.py
+++ b/src/pyproject_fmt/formatter/util.py
@@ -66,9 +66,6 @@ def order_keys(
         for _, elements in sorted(entries.items(), key=sort_inline_table):
             body.extend(elements)
 
-    if isinstance(table, Table):
-        body.append((None, Whitespace("\n")))  # add trailing newline to separate
-
 
 @dataclass
 class ArrayEntries:
@@ -109,8 +106,21 @@ def sorted_array(
     body.append(_ArrayItemGroup(indent=Whitespace("\n")))
 
 
+def ensure_newline_at_end(body: Table) -> None:
+    content = body
+    while content.value.body and isinstance(content.value.body[-1][1], Table):
+        content = content.value.body[-1][1]
+    whitespace = Whitespace("\n")
+    insert_body = content.value.body
+    if insert_body and isinstance(insert_body[-1][1], Whitespace):
+        insert_body[-1] = insert_body[-1][0], whitespace
+    else:
+        insert_body.append((None, whitespace))
+
+
 __all__ = [
     "ArrayEntries",
     "sorted_array",
     "order_keys",
+    "ensure_newline_at_end",
 ]
diff --git a/tests/__init__.py b/tests/__init__.py
index d3cf850..b82d181 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -8,4 +8,6 @@
 
 Fmt = Callable[[Callable[[TOMLDocument, Config], None], str, str], None]
 
-__all__ = ["Fmt"]
+__all__ = [
+    "Fmt",
+]
diff --git a/tests/formatter/test_tools.py b/tests/formatter/test_tools.py
new file mode 100644
index 0000000..3de4cfe
--- /dev/null
+++ b/tests/formatter/test_tools.py
@@ -0,0 +1,50 @@
+from __future__ import annotations
+
+from pyproject_fmt.formatter.tools import fmt_tools
+from tests import Fmt
+
+
+def test_tools_ordering(fmt: Fmt) -> None:
+    content = """
+    [tool.coverage]
+    a = 0
+    [tool.pytest]
+    a = 0
+    [tool.black]
+    a = 0
+    [tool.isort]
+    a = 0
+    [tool.flake8]
+    [tool.hatch]
+    a = 0
+    [tool.setuptools_scm]
+    a = 0
+    [tool.setuptools]
+    a.b = 0
+
+    """
+    expected = """
+    [tool.setuptools]
+    a.b = 0
+
+    [tool.setuptools_scm]
+    a = 0
+
+    [tool.hatch]
+    a = 0
+
+    [tool.black]
+    a = 0
+
+    [tool.isort]
+    a = 0
+
+    [tool.flake8]
+
+    [tool.pytest]
+    a = 0
+
+    [tool.coverage]
+    a = 0
+        """
+    fmt(fmt_tools, content, expected)
diff --git a/tests/test_cli.py b/tests/test_cli.py
index c64bb05..88bfb82 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import os
 import sys
 from pathlib import Path
 from stat import S_IREAD, S_IWRITE
@@ -36,8 +37,10 @@ def test_cli_pyproject_toml_not_exists(tmp_path: Path, capsys: pytest.CaptureFix
 
 
 def test_cli_pyproject_toml_not_file(tmp_path: Path, capsys: pytest.CaptureFixture[str]) -> None:
+    path = tmp_path / "temp"
+    os.mkfifo(path)
     with pytest.raises(SystemExit) as context:
-        cli_args([str(tmp_path)])
+        cli_args([str(path)])
     assert context.value.code != 0
     out, err = capsys.readouterr()
     assert not out
@@ -69,3 +72,8 @@ def test_pyproject_toml_resolved(tmp_path: Path, monkeypatch: pytest.MonkeyPatch
     path.write_text("")
     result = cli_args(["tox.ini"])
     assert result.inputs == [path]
+
+
+def test_pyproject_toml_dir(tmp_path: Path) -> None:
+    (tmp_path / "pyproject.toml").write_text("")
+    cli_args([str(tmp_path)])
diff --git a/tox.ini b/tox.ini
index 8d29c36..070de9e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -44,7 +44,7 @@ description = run type check on code base
 setenv =
     {tty:MYPY_FORCE_COLOR = 1}
 deps =
-    mypy==0.991
+    mypy==1
 commands =
     mypy --strict --python-version 3.10 src tests
 
diff --git a/whitelist.txt b/whitelist.txt
index 80a099e..d335dd8 100644
--- a/whitelist.txt
+++ b/whitelist.txt
@@ -3,19 +3,13 @@ autodoc
 canonicalize
 capsys
 chdir
-conf
-configs
-deps
-difflib
 dunder
 extlinks
-fmt
-formatter
 fromfile
-func
 intersphinx
 iread
 iwrite
+mkfifo
 nitpicky
 pep508
 py38
@@ -23,12 +17,9 @@ pygments
 pyproject
 raws
 readouterr
-req
 sdist
 skipif
-tmp
 tofile
 toml
 tomlkit
 typehints
-util