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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.beads/formulas/rule-of-five.formula.json

@@ -1,32 +0,0 @@
-{
-  "formula": "rule-of-five",
-  "type": "expansion",
-  "description": "Jeffrey Emanuel's discovery: LLM agents produce best work through 4-5 iterative refinements. Breadth-first exploration, then editorial passes.",
-  "version": 1,
-  "template": [
-    {
-      "id": "{target}.draft",
-      "description": "Initial attempt at: {target.description}. Don't aim for perfection. Get the shape right. Breadth over depth."
-    },
-    {
-      "id": "{target}.refine-1",
-      "description": "First refinement pass. Focus: CORRECTNESS. Fix errors, bugs, mistakes. Is the logic sound?",
-      "needs": ["{target}.draft"]
-    },
-    {
-      "id": "{target}.refine-2",
-      "description": "Second refinement pass. Focus: CLARITY. Can someone else understand this? Simplify. Remove jargon.",
-      "needs": ["{target}.refine-1"]
-    },
-    {
-      "id": "{target}.refine-3",
-      "description": "Third refinement pass. Focus: EDGE CASES. What could go wrong? What's missing? Handle the unusual.",
-      "needs": ["{target}.refine-2"]
-    },
-    {
-      "id": "{target}.refine-4",
-      "description": "Final polish. Focus: EXCELLENCE. This is the last pass. Make it shine. Is this something you'd be proud to ship?",
-      "needs": ["{target}.refine-3"]
-    }
-  ]
-}