Properly handle file inclusion/exclusion rules when using -c

A regression introduced in e4f1d427 caused file inclusion/exclusion
rules (like ['AllCops']['Excludes']) to be ignored when specified in
a configuration file passed via -c. This fixes that by correcting the
order of operations.

Fixes #620.
Merge pull request #621 from fancyremarker/fix-external-config-excludes

Properly handle file inclusion/exclusion rules when using -c