Etckeeper checks for possible hardlinks in the file /etc/etckeeper/pre-commit.d/20warn-problem-files

but it doesn't seem to exclude the files that match the ".gitignore" directives.

Tested:

# cat .gitignore | grep -i py
*.pyc
*.pyo


15:12 root@someserver:/etc/fail2ban/action.d
# ls -l smtp.pyc
-rw-r--r-- 2 root root 5921 Jul 13  2017 smtp.pyc

It would be better, for monitoring reasons, to exclude all those files that fall in the .gitignore pattern, as they won't be tracked anyway.