I am trying to use etckeeper to track / (We need to track /etc and also /unionfs/overlay/etc, which is an etc that gets loaded onto a second computer).

git ls-files lists only the files we want to track, and .gitignore correctly excludes all the files we don't want to match (such as ./home, ./proc, ), yet somehow .etckeeper contains metadata for a bunch of files that I don't want etckeeper to touch.