Exclude files deleted from the working tree from all_files - #905

Older Git versions can resurrect staged deletions and old rename paths as untracked files while commit hooks run. The scripted `git stash --keep-index` resets the working tree to HEAD, then restores the index without removing those paths, so tools such as RSpec can discover obsolete files.

Stash normally and restore the staged tree with `git read-tree --reset -u stash@{0}^2`. This updates the index and working tree without moving HEAD. If restoring the staged tree fails, stop before running hooks and retain the stash for recovery. Only restore it when this run actually created a stash.

Fixes the original normal-commit report in #699; the separate `overcommit --run` case was addressed in #905.

The added examples exposed a coverage-reporting problem: round-robin shard assignments shift when tests are added, so per-shard coverage comparisons can fail despite higher total coverage. CI now collects every shard's LCOV report and submits them together for one complete-suite coverage comparison. All test matrix jobs still run, and missing coverage artifacts fail the build.

Validation:

- Full suite: 1,750 examples, zero failures.
- All pre-commit checks and RuboCop pass.
- Added 12 examples covering pre-commit and commit-message contexts, current and emulated legacy stash behavior, complete state restoration, existing stashes, and setup failure recovery. No existing tests were removed.
- Confirmed setup and cleanup against Git 2.20's actual stash script, with its legacy text-output helper restored for compatibility with current Git.
- Confirmed the old-name regression tests fail before the fix.

Fixes #699.

* origin/main: (108 commits)
  Remember all previously approved configurations and hooks (sds#665)
  Keep deleted and renamed paths absent while stashing changes (sds#928)
  Document the case-sensitive KtLint hook name (sds#927)
  Update CI actions and pin Ubuntu to clear annotations (sds#926)
  Preserve standard input bytes when forwarding hooks (sds#925)
  Preserve Git-quoted filenames when running all hooks (sds#924)
  Fail when Git cannot enumerate tracked files (sds#923)
  Add note about disabling default hooks (sds#922)
  Close files inspected by LineEndings (sds#921)
  Use Script Host before PowerShell for Windows parent query fallback (sds#920)
  Cache Windows dependency resolution with daily refreshes (sds#919)
  Avoid PowerShell startup for Windows parent command queries (sds#918)
  Avoid repeated CLI startup when preparing integration fixtures (sds#917)
  Allocate more CI runners to Windows with asymmetric sharding (sds#916)
  Shard CI tests across runners and add one required CI check (sds#915)
  Remove EOL Ruby versions from the CI matrix (sds#914)
  Cut CI test time by 68% while preserving the full test matrix (sds#913)
  Cut version 0.75.0 (sds#912)
  Re-enable the full Windows test matrix and fix platform failures (sds#911)
  Read .overcommit.yml as UTF-8 in the hook template (sds#910)
  Update Overcommit logo (sds#907)
  Cut version 0.74.0 (sds#906)
  Keep each worktree's signatures separate (sds#903)
  Recognize amend aliases on macOS (sds#904)
  Exclude files deleted from the working tree from all_files (sds#905)
  Restore the Ruby 2.6-3.1 test checks (sds#902)
  Delete subprocess output tempfiles once they are read (sds#901)
  Stop wrapping commands in cmd.exe on Windows (sds#898)
  Allow URL-only lines to exceed TextWidth body limit (sds#900)
  Cut version 0.73.0 (sds#896)
  Add automated release flow (sds#895)
  Instruct oxfmt not to fail if no files are matched (sds#894)
  Add filetypes to oxc tools (sds#893)
  Add pre commit hook for herb-lint (sds#892)
  Cut version 0.72.0 (sds#891)
  Remove maintainability badge (sds#890)
  Require patched REXML version (sds#889)
  Fix operation state restoration in linked worktrees (sds#887)
  Fail Flay hook when flay crashes instead of silently passing (sds#885)
  Fix Solargraph regexp capture warning (sds#886)
  Cut version 0.71.0 (sds#883)
  Prepare for the new solargraph typecheck format (sds#873)
  Make hook context input reads thread-safe (sds#882)
  Cut version 0.70.0 (sds#880)
  Add oxc pre-commit hooks (sds#879)
  Add Ruby 3.4 and 4.0 to CI matrix (sds#878)
  Cut version 0.69.0 (sds#877)
  Use Etc.nprocessors and handle sandboxed environments (sds#876)
  Cut version 0.68.0 (sds#872)
  Add solargraph pre-commit hook for typechecking (sds#871)
  Update RuboCop in Gemfile to silence a deprecation warning in build (sds#870)
  Cut version 0.67.1
  adds 'set' requirements to diff hook context. (sds#866)
  Add note about unsupported YAML features in `gemfile:` line in default.yml (sds#865)
  Cut version 0.67.0 (sds#864)
  Restore ability to specify "gemfile: false" in config (sds#863)
  Cut version 0.66.0 (sds#861)
  Add `-diff` cli option for running precommit hooks against diffs (sds#860)
  Cut version 0.65.0
  Load bundled gems on expected version (sds#859)
  Update changelog
  Bump rexml to >= 3.3.9 to resolve GHSA-2rxp-v6pw-ch6m (sds#857)
  Expand tildes(~) for hooksPath (sds#853)
  Fix spec compatibility with recent git versions (sds#854)
  Update changelog
  Cut version 0.64.0 (sds#852)
  Add changelog_uri to gemspec (sds#851)
  Support stylelint 16+, which emits messages on stderr (sds#848)
  Add Ruby 3.3 to CI matrix (sds#849)
  Update README with latest requirements (sds#845)
  Fix README badges (sds#844)
  Cut version 0.63.0 (sds#843)
  Add RSpec Hook to PreCommit, Add Applicable files if set (sds#842)
  Fix RuboCop warnings (sds#841)
  [FEATURE] New pre-commit hook: Sorbet (Issue sds#825) (sds#826)
  Green CI PoC (sds#833)
  Revert "Get suite running smoothly again (sds#824)" (sds#840)
  Get suite running smoothly again (sds#824)
  Cut version 0.62.0 (sds#821)
  Allow childprocess 5 (sds#820)
  Update branch for CI from `master` to `main` (sds#819)
  Update RuboCop (sds#818)
  Adding Ruby 3.2 to test matrix (sds#816)
  Cut version 0.61.0 (sds#817)
  fix: local overcommit file merges with existing .overcommit.yml file (sds#815)
  Allow ReplaceBranch to use skip_if (sds#809)
  Cut version 0.60.0 (sds#807)
  Add non ASCII encoding schema support to RailsSchemaUpToDate hook (sds#786)
  Rescue Psych::DisallowedClass in YamlSyntax (sds#805)
  Add optional additional local configuration (sds#799)
  Add MixTest hook (sds#802)
  Add MixFormat hook (sds#801)
  support trailing space in replace_branch's 'replacement_text' config (sds#804)
  Allow overriding Gemfile.lock (sds#796)
  Cut version 0.59.1 (sds#785)
  Revert addition of `--disable-pending-cops` flag to RuboCop (sds#783)
  Revert `Fix encoding of process output under windows` (sds#784)
  Cut version 0.59.0 (sds#780)
  Partial log flushing to make long hooks intuitive (sds#777)
  Fix pronto hooks swallowing generic errors (sds#779)
  ...

# Conflicts:
#	CHANGELOG.md
#	README.md