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/security-audit.formula.json

@@ -1,35 +0,0 @@
-{
-  "formula": "security-audit",
-  "type": "aspect",
-  "description": "Cross-cutting security concern. Applies security scanning before and after implementation steps.",
-  "version": 1,
-  "pointcuts": [
-    {"glob": "*.implement"},
-    {"glob": "*.submit"}
-  ],
-  "advice": {
-    "around": {
-      "before": [
-        {
-          "id": "security-prescan",
-          "description": "Pre-implementation security check. Review for secrets/credentials in scope. Check dependencies for known vulnerabilities.",
-          "args": {"target": "{step.id}"}
-        }
-      ],
-      "after": [
-        {
-          "id": "security-postscan",
-          "description": "Post-implementation security scan. Scan new code for vulnerabilities (SAST). Check for hardcoded secrets. Review for OWASP Top 10 issues.",
-          "args": {"target": "{step.id}"},
-          "output": {"approved": "boolean", "findings": "list"}
-        },
-        {
-          "gate": {
-            "condition": "security-postscan.output.approved == true",
-            "message": "Security approval required before proceeding"
-          }
-        }
-      ]
-    }
-  }
-}