Fix: Pre-commit hook includes untracked files in commits

[christolis]

Fixes #1039.

With this pull request, untracked files do not get included in commits handled by the pre-commit hook.

Screenshots

[Zabuzard]

I dont quite get the point of this. Untracked files should NOT be automatically included in commits. Otherwise you can not keep files untracked, which can be on purpose (I do this quite often).
@marko-radosavljevic for review please

[marko-radosavljevic]

Blocked until I review and test it, per Daniel's request.

[christolis]

For reference the -A option, found in the original code, works like this (source, emphasis mine):

Update the index not only where the working tree has a file matching but also where the index already has an entry. This adds, modifies, and removes index entries to match the working tree.

If no is given when -A option is used, all files in the entire working tree are updated (old versions of Git used to limit the update to the current directory and its subdirectories).

The -u option in the PR works like this (source, emphasis mine):

Update the index just where it already has an entry matching . This removes as well as modifies index entries to match the working tree, but adds no new files.

If no is given when -u option is used, all tracked files in the entire working tree are updated (old versions of Git used to limit the update to the current directory and its subdirectories).

[tj-wazei]

I have tested and reproduced the issue. It is indeed a bug.

In my test, the following output was provided when running git status:

On branch bug-test
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
        modified:   application/src/main/java/org/togetherjava/tjbot/Application.java

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        application/src/main/java/org/togetherjava/tjbot/BugTest.java

After running git commit -m "test"

This is the result of git status:

On branch bug-test
nothing to commit, working tree clean

The output from the pre-commit hook shows:

****Done pre-commit hooks****
[bug-test 96a2cb1] test
 2 files changed, 6 insertions(+)
 create mode 100644 application/src/main/java/org/togetherjava/tjbot/BugTest.java

Clearly, we can see it's commiting untracked files.

took too long to review