Related bug (maybe the same). Reproduction:
$ git clone git@github.com:jekyll/jekyll.git --no-checkout
Cloning into 'jekyll'...
remote: Counting objects: 41331, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 41331 (delta 0), reused 0 (delta 0), pack-reused 41326
Receiving objects: 100% (41331/41331), 11.91 MiB | 9.15 MiB/s, done.
Resolving deltas: 100% (26530/26530), done.
$ cd jekyll
$ git config core.sparsecheckout true
$ echo 'CONDUCT.markdown' > .git/info/sparse-checkout
$ echo 'Gemfile' >> .git/info/sparse-checkout
$ echo 'Rakefile' >> .git/info/sparse-checkout
$ echo 'appveyor.yml' >> .git/info/sparse-checkout
$ git checkout --
Your branch is up-to-date with 'origin/master'.
$ ls
CONDUCT.markdown Gemfile Rakefile appveyor.yml lib
I was not expecting to see 'lib' in the resulting file list
I didn't say so before - I'm on a Mac, with a homebrew installed Git 2.11.0
- Paul