git pre-commit hook to format and re-add files at the same time

Edited following this answer.

You can format and add your files back within the hook. The problem is that you might have unstaged modifications of staged files. To do this in a clean way you can get the file from index as a tmp, format the tmp and replace the entry in index using the formatted tmp. Here is an approach to something that should solve the problem:

# Regexp for grep to only choose some file extensions for formatting
exts="\.\(ext\|ext2\)$"

# The formatter to use
formatter=`which your_formatter`

# Check availability of the formatter
if [ -z "$formatter" ]
then
  1>&2 echo "$formatter not found. Pre-commit formatting will not be done."
  exit 0
fi

# Format staged files
for file in `git diff --cached --name-only --diff-filter=ACMR | grep $exts`
do
  echo "Formatting $file"
  # Get the file from index
  git show ":$file" > "$file.tmp"
  # Format it
  "$formatter" -i "$file.tmp"
  # Create a blob object from the formatted file
  hash=`git hash-object -w "$file.tmp"`
  # Add it back to index
  git update-index --add --cacheinfo 100644 "$hash" "$file"
  # Remove the tmp file
  rm "$file.tmp"
done

# If no files left in index after formatting - fail
ret=0
if [ ! "`git diff --cached --name-only`" ]; then
  1>&2 echo "No files left after formatting"
  exit 1
fi

You can stash just the unstaged changes using the technique described here. Then run the formatter on just the staged changes and pop the stash. Below pre-commit hook uses clang-format-diff

#!/bin/sh

# stash unstaged changes
git commit --no-verify -m 'Save index'
old_stash=$(git rev-parse -q --verify refs/stash)
git stash push -m 'Unstaged changes'
new_stash=$(git rev-parse -q --verify refs/stash)
git reset --soft HEAD^

# format staged changes
git diff -U0 --no-color --staged HEAD -- '*.java' | $PWD/clang-format-diff.py -i -p1

git add -u
if [ "$old_stash" != "$new_stash" ]; then # if unstaged changes were stashed reapply to working tree
    git stash pop
fi
exit 0

In your pre-commit hook, you need to add your files, so if your hook is something like:

#!/bin/bash
echo 1 > file
exit 0

then you would need to modify it to have the add:

#!/bin/bash
echo 1 > file
git add file
exit 0

To get a list of all modified files, you could use git-ls-files:

git ls-files -m

However, it would be better if you could just get a list from your code of which files are modified or just add all files again. git diff-tree -r --name-only --no-commit-id <tree-ish> should work for you to get a list of all files.

Basically, adding the files again after modifying works because the commit does not occur until after your pre-commit hook runs, so whatever is staged in the working tree at that point is committed.