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Exclude files deleted from the working tree from all_files (#905)

Refs #699: this fixes the `overcommit --run` case narrowed down in
https://github.com/sds/overcommit/issues/699#issuecomment-974406367 and
https://github.com/sds/overcommit/issues/699#issuecomment-974433262. 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... (continued)

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