Fix code quality checks to run on project root and custom libs

Fixes #1600
Fixes #1601

tox.ini

@@ -33,6 +33,15 @@ commands =
 max-line-length = 79
 verbose = 2
 statistics = True
+exclude =
+    .github/
+    .tox/
+    .pytest_cache/
+    htmlcov/
+    logs/
+    libs/common
+    libs/win
+    libs/py2
 ignore =
 ;   -- flake8 --
 ;    E501 line too long
@@ -74,13 +83,13 @@ skip_install = true
 commands =
 ;   ** PRIMARY TESTS **
 ;   Run flake8 tests (with plugins) using default test selections
-    flake8 core tests setup.py
+    flake8
 ;   ** SELECTIVE TESTS **
 ;   Run flake8 tests (with plugins) for specific optional codes defined below
 ;   -- flake8-bugbear --
 ;    B902 Invalid first argument used for instance method.
 ;    B903 Data class should be immutable or use __slots__ to save memory.
-    flake8 core tests setup.py --select=B902,B903
+    flake8 --select=B902,B903
 
 [coverage:run]
 omit =