chore: move Ruff excludes to ruff.extend-exclude (#5112)

Previously, it was in `ruff.lint.exclude`, so exclusions were not
applied to `ruff format`.

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## Summary by CodeRabbit

* **Chores**
* Updated development tooling configuration to enhance code quality
standards and consistency checks.

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settings.</sub>

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Author: njzjz

pyproject.toml

@@ -354,6 +354,11 @@ ignore = "D413, D416, D203, D107, D213"
 profile = "black"
 force_grid_wrap = 1
 
+[tool.ruff]
+extend-exclude = [
+    "source/3rdparty/**",
+]
+
 [tool.ruff.format]
 docstring-code-format = true
 
@@ -397,10 +402,6 @@ ignore = [
     "D404", # TODO: first word of the docstring should not be This
 ]
 
-exclude = [
-    "source/3rdparty/**",
-]
-
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"