Fix exclusion in Flake8 configuration (#16087)

Related to #16071

Summary of the issue:
When linting we exclude certain directories where the code is auto generated. These exclusions are not working (this probably regressed with the Flake8 update, though I haven't checked).

Description of user facing changes
When linting exclusions in Flake8 configuration are once again respected.

Description of development approach
Flake8 considers that paths in the exclusion list are provided relative to the config file location not to the CWD, our exclusions were modified to account for this
After the file was modified I started getting errors due to usage of inline comments, apparently this was never supposed to work, as per this quote from the documentation:
Following the recommended settings for Python’s configparser, Flake8 does not support inline comments for any of the keys. So while this is fine:...

Therefore we no longer use inline comments in the config.

tests/lint/flake8.ini

@@ -27,26 +27,38 @@ max-line-length = 110
 hang-closing = False
 
 ignore =
-	W191,  # indentation contains tabs
-	W503,  # line break before binary operator. We want W504(line break after binary operator)
+	# indentation contains tabs
+	W191,
+	# Line break before binary operator.
+	# We want W504 (line break after binary operator).
+	W503,
 
+# inform flake8 about functions we consider built-in.
+builtins =
+	# translation lookup
+	_,
+	# translation lookup
+	ngettext,
+	# translation lookup
+	pgettext,
+	# translation lookup
+	npgettext,
 
-builtins = # inform flake8 about functions we consider built-in.
-	_, # translation lookup
-	ngettext, # translation lookup
-	pgettext, # translation lookup
-	npgettext, # translation lookup
-
-exclude = # don't bother looking in the following subdirectories / files.
+# don't bother looking in the following subdirectories / files.
+exclude =
 	.git,
 	__pycache__,
 	.tox,
 	build,
 	output,
-	include/*,
-	miscDeps,
-	source/louis,
-	source/comInterfaces/*, # #10924: generated by third-party dependencies
+	# When excluding concrete paths relative to a directory,
+	# not matching multiple folders by name e.g. `__pycache__`,
+	# paths are relative to the configuration file.
+	../../include/*,
+	../../miscDeps,
+	../../source/louis,
+	# #10924: generated by third-party dependencies
+	../../source/comInterfaces/*,
 
 filename =
 	*.py,