fix: add timeout to subprocess calls in context_references

[memosr]

_expand_git_reference() and _rg_files() called subprocess.run() without a timeout. On a large repository, @diff, @StaGeD, or @git:N references could hang the agent indefinitely while git or ripgrep processes slow output.

• Add timeout=30 to git subprocess in _expand_git_reference() with a user-friendly error message on TimeoutExpired
• Add timeout=10 to rg subprocess in _rg_files() returning None on timeout (falls back to os.walk folder listing)

What does this PR do?

Related Issue

Fixes #

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

How to Test

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:

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

For New Skills

• This skill is broadly useful to most users (if bundled) — see Contributing Guide
• SKILL.md follows the standard format (frontmatter, trigger conditions, steps, pitfalls)
• No external dependencies that aren't already available (prefer stdlib, curl, existing Hermes tools)
• I've tested the skill end-to-end: hermes --toolsets skills -q "Use the X skill to do Y"

Screenshots / Logs

[teknium1]

Merged via PR #3469. Cherry-picked clean onto current main with authorship preserved. Thanks @memosr!