refactor: formulas use YAML instead of JSON (gt-8tmz)

- Convert .formula.json files to .formula.yaml
- Update molecule-algebra.md to specify YAML format
- Update molecular-chemistry.md proto examples
- Add Safety Constraints section: cycle detection, aspect
  self-matching prevention, max expansion depth, graceful degradation

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.beads/formulas/shiny.formula.json

@@ -1,35 +0,0 @@
-{
-  "formula": "shiny",
-  "description": "Engineer in a Box - the canonical right way. Design before you code. Review before you ship. Test before you submit.",
-  "version": 1,
-  "vars": {
-    "feature": "{{feature}}",
-    "assignee": "{{assignee}}"
-  },
-  "steps": [
-    {
-      "id": "design",
-      "description": "Think carefully about architecture before writing code. Consider: How does this fit into the existing system? What are the edge cases? What could go wrong? Is there a simpler approach?"
-    },
-    {
-      "id": "implement",
-      "description": "Write the code for {{feature}}. Follow the design. Keep it simple. Don't gold-plate.",
-      "needs": ["design"]
-    },
-    {
-      "id": "review",
-      "description": "Review the implementation. Check for: Does it match the design? Are there obvious bugs? Is it readable and maintainable? Are there security concerns?",
-      "needs": ["implement"]
-    },
-    {
-      "id": "test",
-      "description": "Write and run tests. Unit tests for new code, integration tests if needed, run the full test suite, fix any regressions.",
-      "needs": ["review"]
-    },
-    {
-      "id": "submit",
-      "description": "Submit for merge. Final check: git status, git diff. Commit with clear message. Push and create PR.",
-      "needs": ["test"]
-    }
-  ]
-}