Stash changes while keeping the changes in the working directory in Git

git stash and then git stash apply (git stash && git stash apply) will stash files and apply stash immediately after it. So after all you will have your changes in stash and in working dir.

You can create an alias if you want it in one piece. Just put something like this to ~/.gitconfig:

[alias]
    sta = "!git stash && git stash apply"

The drawback of this approach is that all files are stashed and recreated. This means that timestamps on the files in question will be changed. (Causing Emacs to complain when I try to save the file if opened it before I did the git sta, and may cause unnecessary rebuilds if you're using make or friends.)

For what it's worth, another way to do this is to stage the changes you want to keep, and then stash everything using --keep-index:

$ git add modified-file.txt
$ git stash push --keep-index

The commands above will stash everything, but it will leave the files staged in your working directory.

From the official Linux Kernel Git documentation for git stash or from git-scm:

If the --keep-index option is used, all changes already added to the index are left intact.

You can use git stash create to create a stash commit, and then save it to the stash using git stash store:

git stash store $(git stash create) -m "Stash commit message"

This can be saved to a git alias to make it more convenient:

git config --global alias.stash-keep '!git stash store $(git stash create)'

git stash-keep -m "Stash commit message"

Note that this does not do everything that git stash push does. For instance, it does not append the branch name to the commit, e.g. "stash@{0}: On myBranch: Stash commit message".