Undo git update-index --skip-worktree

If you want to undo all files that was applied skip worktree, you can use the following command:

git ls-files -v | grep -i ^S | cut -c 3- | tr '\012' '\000' | xargs -0 git update-index --no-skip-worktree

1. git ls-files -v will print all files with their status
2. grep -i ^S will filter files and select only skip worktree (S) or skip worktree and assume unchanged (s), -i means ignore case sensitive
3. cut -c 3- will remove status and leave only paths, cutting from the 3-rd character to the end
4. tr '\012' '\000' will replace end of line character (\012) to zero character (\000)
5. xargs -0 git update-index --no-skip-worktree will pass all paths separated by zero character to git update-index --no-skip-worktree to undo

Aha! I simply want:

git update-index --no-skip-worktree <file>

According to http://www.kernel.org/pub/software/scm/git/docs/git-update-index.html, use

git ls-files -v

to see the "assume unchanged" and "skip-worktree" files marked with a special letter. The "skip-worktree" files are marked with S.

Edit: As @amacleod mentioned, making an alias to list all the hidden files is a nice trick to have so that you don't need to remember it. I use alias hidden="git ls-files -v | grep '^S'" in my .bash_profile. It works great!