[desktop] Fix desktop bootstrap existing install pinning

[CHYJ1227]

What does this PR do?

Prevents packaged desktop bootstrap reruns from passing the build-stamp commit to the installer when activeRoot is already a git checkout. Fresh desktop bootstrap installs still receive the exact commit pin, but existing installs now stay on their configured branch during bootstrap repair/update instead of getting detached back to an older packaged stamp after hermes update.

I reproduced this from local desktop logs: bootstrap found an existing installation, updated to a newer HEAD, then immediately passed the packaged commit and ran Pinning checkout to commit ..., which detached the checkout back to the packaged app build stamp.

Related: #39192 also touches desktop install stamps, but it still pins official stamped commits unless commitPinned=false. This focused fix covers existing git checkouts on current main.

Related Issue

No issue filed.

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 🔒 Security fix
• 📝 Documentation update
• ✅ Tests (adding or improving test coverage)
• ♻️ Refactor (no behavior change)
• 🎯 New skill (bundled or hub)

Changes Made

• apps/desktop/electron/bootstrap-runner.cjs: add existing-git-checkout detection and skip commit pins for existing installs while preserving branch args.
• apps/desktop/electron/bootstrap-runner.test.cjs: add regression coverage for fresh installs keeping commit pins and existing checkouts omitting them.

How to Test

1. Start from a packaged desktop app whose install stamp points at an older commit.
2. Ensure ~/.hermes/hermes-agent is an existing git checkout that has been updated beyond that stamp.
3. Trigger desktop bootstrap again; the repository stage should not pass --commit/-Commit, so it should not detach the checkout back to the packaged stamp.

Validation run locally:

• node --test apps/desktop/electron/bootstrap-runner.test.cjs
• npm run test:desktop:platforms --workspace apps/desktop
• npx eslint electron/bootstrap-runner.cjs electron/bootstrap-runner.test.cjs from apps/desktop
• git diff --check
• python3 scripts/check-windows-footguns.py apps/desktop/electron/bootstrap-runner.cjs apps/desktop/electron/bootstrap-runner.test.cjs

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits (fix(scope):, feat(scope):, etc.)
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix/feature (no unrelated commits)
• I've run pytest tests/ -q and all tests pass
• I've added tests for my changes (required for bug fixes, strongly encouraged for features)
• I've tested on my platform: macOS 26.5.1 arm64

Documentation & Housekeeping

• I've updated relevant documentation (README, docs/, docstrings) — N/A
• I've updated cli-config.yaml.example if I added/changed config keys — N/A
• I've updated CONTRIBUTING.md or AGENTS.md if I changed architecture or workflows — N/A
• I've considered cross-platform impact (Windows, macOS) per the compatibility guide
• I've updated tool descriptions/schemas if I changed tool behavior — N/A

Screenshots / Logs

Local log evidence before the fix showed repeated bootstrap repository stages like:

• Existing installation found, updating...
• HEAD is now at <newer branch head>
• Pinning checkout to commit <older packaged stamp>...
• HEAD is now at <older packaged stamp>

[OutThisLife]

Superseded by #61935 (current-main salvage of #59902 / this PR's core idea).

Closing as stale against the ts-ified desktop bootstrap runner.

[OutThisLife]

Superseded by #61935.