When interacting between Windows and Unix filesystems using Git, setting a file to be executable takes a particular Git command from the Windows computer. With standalone Unix systems, just chmod +x myfile.sh is tracked by Git. However, with Windows Subsystem for Linux or Cygwin, this chmod +x change is not tracked if the file resides on a Windows filesystem and not within the WSL internal filesystem. This confusing situation is overcome by this command:

git update-index --chmod=+x myfile.sh

Verify the change to executable permission by:

git status --porcelain=2

which will have output including:

1 M. N… 100644 100755 100755 … myfile.sh