New Issue Checklist

• Updated SwiftLint to the latest version
• I searched for existing GitHub issues

Describe the bug

We've recently updated from 0.39.2 to the latest (0.42) and started getting thousands of errors and warnings in files we excluded with rules we excluded in our config file:

I believe this might be related to the fact we're using the --path flag to direct to our config file, like so:

Pods/SwiftLint/swiftlint --path ../

I've tracked this back to 0.41, since running 0.40.3 doesn't exhibit this issue.

Complete output when running swiftlint --path ../

0.41:

Done linting! Found 7123 violations, 2267 serious in 886 files.

0.40.3:

Done linting! Found 3 violations, 0 serious in 321 files.

Environment

• SwiftLint version (run swiftlint version to be sure)? 0.41
• Installation method used (Homebrew, CocoaPods, building from source, etc)? CocoaPods
• Paste your configuration file:

Proprietary, but happy to paste specific portions you think might be an issue.

• Are you using nested configurations?
  No
• Which Xcode version are you using (check xcodebuild -version)? 12.3
• Do you have a sample that shows the issue? I don't - can probably try to figure something out with our structure.