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

JSON for consistency with beads (issues.jsonl, molecules.jsonl).
Agents create/manage formulas; humans use visualizers.

- Simpler parsing (Go built-in JSON)
- No YAML gotchas
- Agents generate JSON flawlessly

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

@@ -0,0 +1,32 @@
+{
+  "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"]
+    }
+  ]
+}

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

@@ -1,61 +0,0 @@
-# rule-of-five.formula.yaml
-# Jeffrey's Rule: Agents converge on best output in 4-5 iterations
-# Breadth-first cognition, then editorial passes
-
-formula: rule-of-five
-type: expansion
-description: |
-  Jeffrey Emanuel's discovery: LLM agents (and humans) produce their best
-  work through iterative refinement. The first pass is breadth-first
-  exploration; subsequent passes are editorial refinement.
-
-  Apply this to any step that benefits from iteration:
-  - Writing (code, docs, plans)
-  - Analysis (reviews, investigations)
-  - Design (architecture, interfaces)
-
-  The expansion replaces one step with five sequential steps.
-version: 1
-
-# This is a macro/expansion template
-# When applied to a target step, it expands to 5 steps
-
-template:
-  - id: "{target}.draft"
-    description: |
-      Initial attempt at: {target.description}
-
-      Don't aim for perfection. Get the shape right.
-      Breadth over depth. Explore the space.
-
-  - id: "{target}.refine-1"
-    description: |
-      First refinement pass. Focus: CORRECTNESS.
-
-      Review the draft. Fix errors, bugs, mistakes.
-      Is the logic sound? Are the facts right?
-    needs: ["{target}.draft"]
-
-  - id: "{target}.refine-2"
-    description: |
-      Second refinement pass. Focus: CLARITY.
-
-      Can someone else understand this?
-      Simplify. Remove jargon. Add explanations where needed.
-    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 inputs, the error paths, the corner cases.
-    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"]

.beads/formulas/security-audit.formula.json

@@ -0,0 +1,35 @@
+{
+  "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"
+          }
+        }
+      ]
+    }
+  }
+}

.beads/formulas/security-audit.formula.yaml

@@ -1,48 +0,0 @@
-# security-audit.formula.yaml
-# AOP aspect for security scanning at implementation boundaries
-
-formula: security-audit
-type: aspect
-description: |
-  Cross-cutting security concern. Applies security scanning
-  before and after implementation steps.
-
-  This is an ASPECT - it doesn't run standalone. Apply it
-  to other formulas using --with-aspect.
-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
-          - Verify security requirements are understood
-        args:
-          target: "{step.id}"
-
-    after:
-      - id: security-postscan
-        description: |
-          Post-implementation security scan.
-
-          - Scan new code for vulnerabilities (SAST)
-          - Check for hardcoded secrets
-          - Verify auth/authz patterns
-          - 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"

.beads/formulas/shiny-enterprise.formula.json

@@ -0,0 +1,53 @@
+{
+  "formula": "shiny-enterprise",
+  "extends": "shiny",
+  "description": "Enterprise-grade engineering workflow. Shiny + Rule of Five + Security + Performance Testing + Review Loop.",
+  "version": 1,
+  "compose": [
+    {
+      "expand": {
+        "target": "implement",
+        "with": "rule-of-five"
+      }
+    },
+    {
+      "aspect": {
+        "pointcut": "implement.*",
+        "with": "security-audit"
+      }
+    },
+    {
+      "gate": {
+        "before": "submit",
+        "condition": "security-postscan.approved == true",
+        "message": "Cannot submit without security approval"
+      }
+    },
+    {
+      "branch": {
+        "from": "implement.refine-4",
+        "steps": [
+          {"id": "perf-test", "description": "Run performance benchmarks"},
+          {"id": "load-test", "description": "Run load/stress tests"},
+          {"id": "chaos-test", "description": "Run chaos engineering tests"}
+        ],
+        "join": "review"
+      }
+    },
+    {
+      "loop": {
+        "step": "review",
+        "until": "review.output.approved == true",
+        "max": 3,
+        "on-max": "escalate"
+      }
+    },
+    {
+      "advice": {
+        "target": "*",
+        "before": {"id": "log-start", "description": "Log: Starting {step.id}"},
+        "after": {"id": "log-end", "description": "Log: Completed {step.id}"}
+      }
+    }
+  ]
+}

.beads/formulas/shiny-enterprise.formula.yaml

@@ -1,66 +0,0 @@
-# shiny-enterprise.formula.yaml
-# Full enterprise engineering workflow with all the bells and whistles
-
-formula: shiny-enterprise
-extends: shiny
-description: |
-  Enterprise-grade engineering workflow.
-
-  Builds on Shiny with:
-  - Rule of Five on implementation (5x refinement)
-  - Security scanning (pre and post)
-  - Performance testing branch
-  - Review loop until approved
-  - Full logging
-
-  Cook this to get a ~30 step proto ready for serious work.
-version: 1
-
-compose:
-  # Apply Rule of Five to the implement step
-  # This expands implement → 5 steps: draft, refine-1..4
-  - expand:
-      target: implement
-      with: rule-of-five
-
-  # Apply security aspect to all implementation steps
-  # Adds security-prescan before and security-postscan after
-  - aspect:
-      pointcut: "implement.*"
-      with: security-audit
-
-  # Gate on security approval before submit
-  - gate:
-      before: submit
-      condition: "security-postscan.approved == true"
-      message: "Cannot submit without security approval"
-
-  # Parallel performance testing branch
-  # These run in parallel after implementation, before review
-  - branch:
-      from: implement.refine-4
-      steps:
-        - id: perf-test
-          description: Run performance benchmarks
-        - id: load-test
-          description: Run load/stress tests
-        - id: chaos-test
-          description: Run chaos engineering tests (fault injection)
-      join: review
-
-  # Loop review until approved (max 3 attempts)
-  - loop:
-      step: review
-      until: "review.output.approved == true"
-      max: 3
-      on-max: escalate
-
-  # Logging on all steps (AOP-style advice)
-  - advice:
-      target: "*"
-      before:
-        - id: log-start
-          description: "Log: Starting {step.id}"
-      after:
-        - id: log-end
-          description: "Log: Completed {step.id} with status {step.status}"

.beads/formulas/shiny.formula.json

@@ -0,0 +1,35 @@
+{
+  "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"]
+    }
+  ]
+}

.beads/formulas/shiny.formula.yaml

@@ -1,67 +0,0 @@
-# shiny.formula.yaml
-# Engineer in a Box - the canonical right way to do engineering
-# Named for Mad Max: "Shiny and chrome!"
-
-formula: shiny
-description: |
-  The canonical engineering workflow. Design before you code.
-  Review before you ship. Test before you submit.
-
-  This is what "doing it right" looks like.
-version: 1
-
-vars:
-  feature: "{{feature}}"           # What you're building
-  assignee: "{{assignee}}"         # Who's doing the work
-
-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?
-
-      Output a brief design doc or notes.
-
-  - id: implement
-    description: |
-      Write the code for {{feature}}.
-
-      Follow the design. Keep it simple. Don't gold-plate.
-      Write code that's easy to review.
-    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 (or merge directly if crew)
-      - Notify relevant parties
-    needs: [test]

docs/molecule-algebra.md

@@ -54,45 +54,37 @@ deterministic.
 
 ### Formula Format
 
-Formulas are YAML files with `.formula.yaml` extension:
+Formulas are JSON files with `.formula.json` extension. JSON for consistency
+with beads (agents create/manage these; humans use visualizers):
 
-```yaml
+```json
-# shiny.formula.yaml
+{
-formula: shiny
+  "formula": "shiny",
-description: Engineer in a Box - the canonical right way
+  "description": "Engineer in a Box - the canonical right way",
-version: 1
+  "version": 1,
-
+  "steps": [
-steps:
+    {"id": "design", "description": "Think carefully about architecture"},
-  - id: design
+    {"id": "implement", "needs": ["design"]},
-    description: Think carefully about architecture
+    {"id": "review", "needs": ["implement"]},
-  - id: implement
+    {"id": "test", "needs": ["review"]},
-    needs: [design]
+    {"id": "submit", "needs": ["test"]}
-  - id: review
+  ]
-    needs: [implement]
+}
-  - id: test
-    needs: [review]
-  - id: submit
-    needs: [test]
 ```
 
 Formulas with composition:
 
-```yaml
+```json
-# shiny-enterprise.formula.yaml
+{
-formula: shiny-enterprise
+  "formula": "shiny-enterprise",
-extends: shiny
+  "extends": "shiny",
-version: 1
+  "version": 1,
-
+  "compose": [
-compose:
+    {"expand": {"target": "implement", "with": "rule-of-five"}},
-  - expand:
+    {"aspect": {"pointcut": "implement.*", "with": "security-audit"}},
-      target: implement
+    {"gate": {"before": "submit", "condition": "security-postscan.approved"}}
-      with: rule-of-five
+  ]
-  - aspect:
+}
-      pointcut: "implement.*"
-      with: security-audit
-  - gate:
-      before: submit
-      condition: "security-postscan.approved"
 ```
 
 ### CLI