Switch to per-file-ignores in config

It seems that '# flake: noqa' disables everything for the file even if
include specific codes to disable and expect the rest to apply. This
seems more successful at just disabling particular codes. Oddly not
documented (that I could find) but covered here:

  https://stackoverflow.com/a/54454433/98555

breathe/parser/index.py

@@ -1,4 +1,3 @@
-# flake8: noqa: E305
 """
 Generated Mon Feb  9 19:08:05 2009 by generateDS.py.
 """

setup.cfg

@@ -3,8 +3,10 @@ license_file = LICENSE
 
 [flake8]
 max-line-length = 100
-exclude=compoundsuper.py,indexsuper.py
+exclude = compoundsuper.py,indexsuper.py
 extend-ignore = E203, E231
+per-file-ignores =
+    breathe/parser/index.py:E305
 
 [bdist_wheel]
 universal = 0