[ybai08]

Refs #699: this fixes the overcommit --run case narrowed down in #699 (comment) and #699 (comment). The renamed-file behaviour in the original report (during a normal commit) is not changed here.

GitRepo.all_files returns everything git ls-files lists. That includes a tracked file that has been deleted from the working tree when the deletion is not staged yet. overcommit --run uses all_files as its list of modified files, so every hook that reads its applicable_files then fails on that path. With JsonSyntax enabled:

$ rm a.json      # tracked, deletion not staged
$ overcommit --run
Running pre-commit hooks
Validate JSON syntax.....................................[JsonSyntax] FAILED
Hook raised unexpected error
No such file or directory @ rb_sysopen - .../a.json

all_files now drops the paths git ls-files --deleted reports. This uses Git's own view rather than File.exist?, so a tracked broken symlink is still listed (the BrokenSymlinks hook needs it). included_files (used by the pre-push Minitest hook) goes through all_files too, so it no longer passes a deleted file either.

Tests

A new context in spec/overcommit/git_repo_spec.rb deletes a committed file without staging the deletion and checks that all_files no longer includes it but still includes the other files.

Run on macOS with Ruby 4.0.7 and Git 2.54.0:

• bundle exec rspec spec/overcommit/git_repo_spec.rb -e '.all_files': 4 examples, 1 failure with lib/overcommit/git_repo.rb from main (the new "is expected not to include .../tracked" example), 4 examples, 0 failures with the change.
• Manual check in a scratch repository with only JsonSyntax enabled, a committed a.json deleted from the working tree, then overcommit --run: main fails with No such file or directory @ rb_sysopen; with the change, [JsonSyntax] OK.
• bundle exec rspec: 1659 examples, 4 failures. The same 4 examples fail on main: the git alias #amendment? examples in hook_context/commit_msg_spec.rb:134,140 and hook_context/pre_commit_spec.rb:43,49, which look specific to this machine's Git (Apple Git).
• bundle exec rubocop: no offenses.

Not run: anything on Windows or Linux.

[ybai08]

The four failing rspec jobs (Ruby 2.6, 2.7, 3.0, 3.1) fail in the "Set up Ruby" step, before any spec runs: Unavailable version 3.1.7 for ruby on ubuntu-26.04 (and the same for 2.6.10, 2.7.8 and 3.0.7). The runner image no longer offers those Rubies. The newer Ruby jobs pass.