How to create file execute mode permissions in Git on Windows?

There's no need to do this in two commits, you can add the file and mark it executable in a single commit:

C:\Temp\TestRepo>touch foo.sh

C:\Temp\TestRepo>git add foo.sh

C:\Temp\TestRepo>git ls-files --stage
100644 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0       foo.sh

As you note, after adding, the mode is 0644 (ie, not executable). However, we can mark it as executable before committing:

C:\Temp\TestRepo>git update-index --chmod=+x foo.sh

C:\Temp\TestRepo>git ls-files --stage
100755 e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 0       foo.sh

And now the file is mode 0755 (executable).

C:\Temp\TestRepo>git commit -m"Executable!"
[master (root-commit) 1f7a57a] Executable!
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100755 foo.sh

And now we have a single commit with a single executable file.

If the files already have the +x flag set, git update-index --chmod=+x does nothing and git thinks there's nothing to commit, even though the flag isn't being saved into the repo.

You must first remove the flag, run the git command, then put the flag back:

chmod -x <file>
git update-index --chmod=+x <file>
chmod +x <file>

then git sees a change and will allow you to commit the change.

---

Required git config for the committer (credit: Nabi’s answer):

git config core.filemode false

Required git config for the cloner:

git config --global core.autocrlf input

Indeed, it would be nice if git-add had a --mode flag

git 2.9.x/2.10 (Q3 2016) actually will allow that (thanks to Edward Thomson):

git add --chmod=+x -- afile
git commit -m"Executable!"

That makes the all process quicker, and works even if core.filemode is set to false.

See commit 4e55ed3 (31 May 2016) by Edward Thomson (ethomson).
Helped-by: Johannes Schindelin (dscho).
^{(Merged by Junio C Hamano -- gitster -- in commit c8b080a, 06 Jul 2016)}

add: add --chmod=+x / --chmod=-x options

The executable bit will not be detected (and therefore will not be set) for paths in a repository with core.filemode set to false, though the users may still wish to add files as executable for compatibility with other users who do have core.filemode functionality.
For example, Windows users adding shell scripts may wish to add them as executable for compatibility with users on non-Windows.

Although this can be done with a plumbing command (git update-index --add --chmod=+x foo), teaching the git-add command allows users to set a file executable with a command that they're already familiar with.