Remove unused ruff exemptions. NFC (#1797)

Remove rules from `lint.ignore` that currently have zero violations, and
remove stale `lint.per-file-ignores` entries for files that do not exist
in this repository.

pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
index 3dc6610..28e412f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,49 +31,32 @@
 lint.external = [ "D" ]
 lint.ignore = [
   "assert-false", # See https://github.com/PyCQA/flake8-bugbear/issues/66
-  "function-uses-loop-variable",
-  "star-arg-unpacking-after-keyword-arg",
   "module-import-not-at-top-of-file",
   "line-too-long",
-  "type-comparison",
-  "ambiguous-variable-name",
   "indentation-with-invalid-multiple", # Does not seem to honor `indent-width = 2` above
   "indentation-with-invalid-multiple-comment", # Does not seem to honor `indent-width = 2` above
   "try-except-in-loop",
-  "manual-list-comprehension",
   "import-outside-top-level",
   "too-many-public-methods",
   "too-many-statements",
-  "too-many-boolean-expressions",
   "too-many-nested-blocks",
-  "redefined-argument-from-local",
   "collapsible-else-if",
   "no-self-use",
-  "global-variable-not-assigned",
   "global-statement",
   "too-many-locals",
   "subprocess-run-without-check",
   "unspecified-encoding",
-  "redefined-loop-name",
   "unraw-re-pattern", # https://docs.astral.sh/ruff/rules/unraw-re-pattern/
   "format-literals", # TODO
   "printf-string-formatting", # TODO
   "f-string", # TODO
   "too-many-statements-in-try-clause",
 ]
-lint.per-file-ignores."emrun.py" = [ "misplaced-bare-raise" ]
-lint.per-file-ignores."tools/ports/*.py" = [ "unused-function-argument", "unused-lambda-argument" ]
-lint.per-file-ignores."test/other/ports/*.py" = [ "unused-function-argument" ]
-lint.per-file-ignores."test/parallel_testsuite.py" = [ "unused-method-argument" ]
-lint.per-file-ignores."test/test_benchmark.py" = [ "unused-method-argument" ]
-lint.mccabe.max-complexity = 51 # Recommended: 10
+lint.mccabe.max-complexity = 41 # Recommended: 10
 lint.pylint.allow-magic-value-types = [
   "bytes",
   "float",
   "int",
   "str",
 ]
-lint.pylint.max-args = 15 # Recommended: 5
-lint.pylint.max-branches = 50 # Recommended: 12
-lint.pylint.max-returns = 16 # Recommended: 6
-lint.pylint.max-statements = 142 # Recommended: 50
+lint.pylint.max-branches = 29 # Recommended: 12