refactor: migrate commit_all and create_evolution_backup staging to git2, kill git_command wrapper

[Scott McMaster (scottmcmaster)]

Summary

This is the last change before we can get rid of the GitCommand CLI wrapper struct, namely to port commit_allover to git2. The biggest change was in staging, so that gets is own helper. Added several unit tests to verify the previous behavior provided by flags in the old CLI command implementation (around signing, names, hooks).

Test Plan

Existing and new unit tests pass.

• No test plan needed

Docs

• Docs updated (companion PR in darkmatter/nixmac-web: #___)
• No docs update needed

[Scott McMaster (scottmcmaster)]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• refactor: migrate commit_all and create_evolution_backup staging to git2, kill git_command wrapper #319 👈 (View in Graphite)
• refactor: migrate checkout_files_at_commit, restore_all, and restore_from_branch_ref to git2 #311
• develop

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[github-actions]

📋 PR Overview

Lines changed	373 (+256 / -117)
Files	0 added, 2 modified, 0 deleted
Draft / WIP	no
Has Test Plan	yes
No Test Plan Needed	no
New UI components	no
New Storybook stories	no
New Rust modules	no
New TS source files	no
New tests	no
package.json touched	no
Cargo.toml touched	no
Infra / CI touched	no

🔬 Coverage

Report	Lines	Statements	Functions	Branches
apps/native/coverage/coverage-summary.json	25.9%	26.1%	24.2%	17.7%

Generated by 🚫 dangerJS against db9b747

[Copilot]

Pull request overview

This PR completes the migration away from the GitCommand CLI wrapper by porting commit_all (and the staging portion of create_evolution_backup) to git2/libgit2, aligning git mutations around repository object/index operations rather than shelling out to git.

Changes:

• Removed the GitCommand/git_command() CLI wrapper from the git execution layer.
• Added a shared stage_all() helper that emulates git add -A using git2 index operations, and used it in commit_all and create_evolution_backup.
• Added unit tests covering commit identity, staging semantics (including ignored/untracked/tracked deletions), nested-directory invocation behavior, and hook non-execution.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
apps/native/src-tauri/src/git/query.rs	Minor doc/comment adjustment in query-layer ref/HEAD resolution notes.
apps/native/src-tauri/src/git/exec.rs	Migrates commit_all + backup staging to git2 via stage_all(), removes CLI wrapper, and adds targeted unit tests for prior CLI semantics.

[cooper (czxtm)]

🙌