Git-hook: No staged changes when running `git commit -a`

Question

Here's my (simplified, no error checking) git hook:

git diff --cached | clang-format-diff -p1 > $PATCHFILE
git patch-apply -p0 $PATCHFILE           # modify the working tree
git patch-apply -p0 --cached $PATCHFILE  # modify what is staged

This works fine, however, when a user is running git commit -a, the documentation to git diff informs me that "there are various ways to check your working tree":

$ git diff            (1)
$ git diff --cached   (2)
$ git diff HEAD       (3)

Changes in the working tree not yet staged for the next commit.

Changes between the index and your last commit; what you would be committing if you run "git commit" without "-a" option.

Changes in the working tree since your last commit; what you would be committing if you run "git commit -a"

As a consequence, the script does not work when a using is git commit -a. This is because it gets called at a stage where the index apparently has not had the changes added.

I would like to apply the clang-format-diff changes only on staged files.

Question:

1. Why, apparently, does git commit -a call the pre-commit hook before staging files? Isn't that a bug?
2. What should I do? Can I somehow detect inside the pre-commit hook that I am inside a git commit -a situation? I would rather avoid formatting unstaged changes.

Notes

• I am using git 2.11.0.
• Related questions but not duplicate:
  • git commit -a bypasses git hook when it shouldn't
  • `git diff` does not work when run from a git pre-commit hook
  • git pre-commit hook not running when running git commit -a