Exclude ".git" directories anywhere. This avoids spurious errors in git
checkouts that contain branch names that look like a file
check-files.py would check. Fix#1713
Exclude "mbed-os" anywhere and "examples" from the root. Switch to the
new mechanism to exclude "yotta/module". These are directories where
we store third-party files that do not need to match our preferences.
Exclude "cov-int" from the root. Fix#1691
