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.
I don't support using etckeeper to version control stuff other than /etc.
30store-metadata gets a list of all fils git is configured to ignore, and then runs a find and uses grep to exclude files in that list.
I've verified this seems to work ok when etckeeper is used the usual way in /etc. Something about the non-supported way you're using etckeeper must be causing the problem.
Perhaps git ls-files -oi --exclude-standard when run in / somehow doesn't list every single file in your entire computer, for whatever reason. When I tried putting a git repo in /.git/ and running that, it hung for a long time.
Sorry, I'm going to close this.