docs(env): mark MESSAGING_CWD as deprecated compatibility fallback

[LeonSGP43]

What does this PR do?

Clarifies that MESSAGING_CWD is only a backward-compat path and that terminal.cwd in config is the canonical setting.

Related Issue

Fixes #5200

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 website/docs/reference/environment-variables.md
• aligned the docs with current Hermes behavior for this specific issue
• kept the change isolated to a single documentation concern

How to Test

1. Review website/docs/reference/environment-variables.md and confirm the wording matches the current behavior described in the issue.
2. Run git diff --check.
3. Run the local proof gate used for this branch:
   • UV_PYTHON=3.11 /Library/Frameworks/Python.framework/Versions/3.10/bin/uv run --frozen pytest -q -o addopts='' tests/hermes_cli/test_plugins_cmd.py
   • UV_PYTHON=3.11 /Library/Frameworks/Python.framework/Versions/3.10/bin/uv run --frozen ruff check tests/hermes_cli/test_plugins_cmd.py
   • env -i HOME="$HOME" PATH="/Library/Frameworks/Python.framework/Versions/3.10/bin:/usr/local/bin:/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin" UV_PYTHON=3.11 /Library/Frameworks/Python.framework/Versions/3.10/bin/uv run --frozen pytest --collect-only -q -o addopts='' tests/hermes_cli/test_plugins_cmd.py

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

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

N/A

[teknium1]

Superseded by #22050, which was merged to main as part of the Bucket-1 docs-correctness sweep (PR #34781). Your PR fixed the same issue — the MESSAGING_CWD deprecation sweep — and the merged version preserves per-commit authorship for the contributor whose variant was the most complete. Both contributors are credited. Thanks for catching this!