refactor: migrate intent_add_untracked to git2, setting INTENT_TO_ADD flag without shelling out

[Scott McMaster (scottmcmaster)]

Summary

Port intent_add_untracked from CLI to git2, with comments noting a few minor complexities.

Test Plan

Existing unit tests (of which there were some) passed, also added a couple new tests, and did manual testing with things like "add a new .nix file to my configuration" and verify that it passes build check and build.

• No test plan needed

Docs

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

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[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
• refactor: migrate checkout_files_at_commit, restore_all, and restore_from_branch_ref to git2 #311
• refactor: migrate intent_add_untracked to git2, setting INTENT_TO_ADD flag without shelling out #310 👈 (View in Graphite)
• refactor: remove git stash command and related functionality #291
• refactor: migrate create_evolution_backup internals to git2, remove get_head_sha wrapper #290
• refactor: migrate tag_commit to git2, remove unused delete_backup_branch #289
• refactor: update file_diff_contents to use git2 instead of CLI, make path helper more robust #283
• refactor: port the git log function from CLI to git2 #281
• refactor: nix-files feedback reusing git status, eliminate resulting dead code #278
• fix: split made_edit_or_build_check into separate flags and minor whitespace cleanup #288
• develop

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[Copilot]

Pull request overview

This PR refactors intent_add_untracked (used to make untracked config files visible to Nix flake evaluation) to use git2 instead of shelling out to the Git CLI, and expands unit test coverage for the new behavior.

Changes:

• Replaced CLI-based discovery (git ls-files --others) and intent staging (git add -N) with a git2 implementation that sets INTENT_TO_ADD index entries pointing at the empty blob.
• Added unit tests verifying the INTENT_TO_ADD flag behavior, ignored-file filtering, and support for repos without a HEAD commit.
• Minor formatting cleanups in existing tests.

[github-actions]

📋 PR Overview

Lines changed	241 (+209 / -32)
Files	0 added, 1 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	26.3%	26.5%	24.3%	17.9%

Generated by 🚫 dangerJS against 25a56f9

[graphite-app]

Merge activity

• Jun 5, 12:29 AM UTC: czxtm added this pull request to the Graphite merge queue.
• Jun 5, 12:30 AM UTC: CI is running for this pull request on a draft pull request (#318) due to your merge queue CI optimization settings.
• Jun 5, 12:33 AM UTC: The Graphite merge queue removed this pull request due to downstack failures on PR #281.
• Jun 5, 12:33 AM UTC: The Graphite merge queue removed this pull request due to downstack failures on PR #281.
• Jun 5, 1:30 AM UTC: czxtm added this pull request to the Graphite merge queue.
• Jun 5, 1:31 AM UTC: CI is running for this pull request on a draft pull request (#321) due to your merge queue CI optimization settings.
• Jun 5, 1:37 AM UTC: Merged by the Graphite merge queue via draft PR: #321.