You have to use "git add" on a bunch of files that you have used "git add" on before.
As far as I can tell, every other revision control system tracks a file for "commit" once it has had even a single "add". This is the default case and what 99% of people want--"I told you to keep track of the file. Now keep track of it until I tell you otherwise."
git is the only revision control system I know of where I have to "git add" the same file over and over and over and over ... before doing "git commit".
But that is fairly standard git UI practice--"Optimize the 1% case and make the 99% case annoying."
It will however nuke changes that are not committed. Which is exactly what I use it for... But your script sounds like a decent solution if you want also that to be undoable