Clean up mention of manual hook stage

This is no longer used. No pre-commit hook specifies it anymore in
`stages`, since 517f83a (gitpython-developers#1865). See b059cd5 (gitpython-developers#1868) for context.

In the lint.yml GitHub Actions workflow, this removes the
extra_args key altogether, because all that would remain there is
--all-files, which is already the default for that action, when
the extra_args key is absent.

.github/workflows/lint.yml

@@ -14,5 +14,3 @@ jobs:
         python-version: "3.x"
 
     - uses: pre-commit/action@v3.0.1
-      with:
-        extra_args: --all-files --hook-stage manual

tox.ini

@@ -12,7 +12,7 @@ commands = pytest --color=yes {posargs}
 [testenv:lint]
 description = Lint via pre-commit
 base_python = py{39,310,311,312,38,37}
-commands = pre-commit run --all-files --hook-stage manual
+commands = pre-commit run --all-files
 
 [testenv:mypy]
 description = Typecheck with mypy