Support hook side effects without stashing repository changes - #939

Pre-commit and commit-msg hooks can now modify, create, remove, and stage files without losing their changes during cleanup. Unstaged edits are saved to a durable binary patch and hidden with a reverse application; cleanup reapplies that patch without changing HEAD, the index, the stash, or merge/cherry-pick metadata. Hooks retain native Git behavior: only edits they explicitly stage enter the commit, and their edits survive failed or interrupted runs.

If restoration conflicts with hook edits, the commit fails while preserving both the hook changes and a patch with recovery instructions. Patches survive garbage collection and forced termination, and successful cleanup removes them. File modification times are restored for unchanged files while hook edits remain visible to watchers.

The existing behavior tests remain, including deletion/rename and configuration-error recovery regressions. Tests tied to stash commands and legacy stash emulation were replaced with patch failure and recovery tests. New regression coverage includes actual commits, first commits, hook failures/exceptions/interruptions, index changes, alternate indexes, worktrees, binary files, unusual paths, symlinks/type changes, CRLF conversion, executable modes, conflicting edits, and shell-safe recovery commands. Interrupt messages now describe patch recovery instead of pointing to the stash. AGENTS.md and contributor guidance require 100% line coverage; CI now enforces it after combining all shard/platform reports.

Validation:

• Complete local suite: 2,169 examples, 0 failures.
• Local exact coverage gate: 3,844/3,844 executable lines (100%).
• bundle exec overcommit --run: passed, including RuboCop.
• All 21 GitHub checks passed, including Ruby 3.3/3.4/4.0 on Linux and Windows, the final CI gate, and Coveralls. Combined CI coverage: 3,846/3,846 executable lines (100%).

This removes the stash/reset mechanisms behind reports such as #65, #80, #135, #168, #372, #524, and #669. lint-staged's current backup/revert workflow still uses stashes and hard resets, so it was not copied.

Closes #238.