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/security-audit.formula.yaml

@@ -0,0 +1,31 @@
+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