What does this PR do?

Fixes config migration data loss during upgrades. The migration now checks missing config fields against the raw on-disk config instead of a defaults-merged config, so user-set values are not overwritten by default placeholders.

It also preserves legacy config shapes by migrating root cwd/backend into terminal.* and expanding legacy flat auxiliary.provider/model values into per-task auxiliary config.

Related Issue

Fixes #17182

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

• Updated hermes_cli/config.py so migration preserves raw user config values during version bumps.
• Added migration helpers for legacy root cwd/backend aliases and flat auxiliary.provider/model fields.
• Added regression tests in tests/hermes_cli/test_config.py for preserving terminal.cwd, timezone, and auxiliary model fields.

How to Test

1. Create a v17 config with absolute terminal.cwd, timezone, and explicit auxiliary.*.model values.
2. Run migrate_config(interactive=False, quiet=True).
3. Verify those values are preserved and _config_version updates to the latest version.

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: Ubuntu/Linux

Documentation & Housekeeping

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

Screenshots / Logs

python3 -m pytest tests/hermes_cli/test_config.py -q -o addopts=''
52 passed, 1 warning in 7.04s