I mistakenly added files using the command

git add file

I have not yet run git commit.

Is there a way to undo this or remove these files from the commit?

You want:

git rm --cached <added_file_to_undo>

Reasoning:

Also a newbie I first tried

git reset .

(to undo my entire initial add) only to get this (not so) helpful message:

fatal: Failed to resolve 'HEAD' as a valid ref.

turns out that this is because the HEAD ref (branch?) doesn't exist until after the first commit. That is, you'll run into the same newbie problem as me if your workflow, like mine, was something like:

1. cd to my great new project directory to try out git, the new hotness
2. git init
3. git add .
4. git status ... lots of crap scrolls by ... => Damn, I didn't want to add all of that.
5. google "undo git add" => find Stackoverflow - yay
6. git reset . => fatal: Failed to resolve 'HEAD' as a valid ref. it further turns out that there's a bug logged against the unhelpfulness of this in the mailing list. And that the correct solution was right there in the git status output (which, yes, I glossed over as 'crap)

... # Changes to be committed: # (use "git rm --cached ..." to unstage) ...

And the solution indeed is to use git rm --cached FILE

Note the warnings elsewhere here - git rm deletes your local working copy of the file, but not if you use --cached. Here's the result of git help rm`:

--cached Use this option to unstage and remove paths only from the index. Working tree files, whether modified or not, will be left.

I proceed to use

git rm --cached .

to remove everything and start again. Didn't work though, because while add . is recursive, turns out rmneeds -r to recurse. sigh.

git rm -r --cached .

Okay, now I'm back to where I started. Next time I'm going to use -n to do a dry run and see what will be added:

git add -n .

UPDATE Oh yeah forgot to mention - I zipped up everything to a safe place before trusting git help rmabout the --cached not destroying anything (and what if I misspelled it)