fix: Correct flake8 config

- Add exclude pattern for flake8 when running with pre-commit as it does
  not fully honor the exclude paths.
- Cleanup exclude paths for flake8 in tox.ini
- Re-enable line length check and correct three affected files

tox.ini

@@ -16,7 +16,7 @@ deps =
     -r{toxinidir}/requirements-extra.txt
 
 [flake8]
-exclude = .tox,env,build,cocoalib,cocoa,help,./qt/dg_rc.py,cocoa/run_template.py,./pkg
+exclude = .tox,env*,build,help,qt/dg_rc.py,pkg
 max-line-length = 120
 select = C,E,F,W,B,B950
-extend-ignore = E203, E501, W503
+extend-ignore = E203,W503