I noticed this on a repo I'm developing that has 4 submodules. When the CI runs

cpp-linter --files-changed-only=false

All the submodules are crawled as if they're part of the current repo's original sources.

Moving the algorithm that detects submodules from list_source_files() into parse_ignored_option() should fix this, but I have to be careful to consider if the user explicitly specifies a submodule to be not ignored.