fix: Remove YAML usage, standardize on JSON/TOML

- Delete 5 legacy .formula.yaml files (have .toml replacements)
- Remove unused FileConfigYAML constant
- Add TODO for beads config.yaml → config.json migration (bd-10wg)
- Update docs to use JSON examples instead of yaml code blocks
- Change plugin frontmatter from YAML to TOML in docs
- Add .toml to code file detection in branch_check.go

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

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

internal/cmd/gitinit.go

@@ -109,7 +109,7 @@ const HQGitignore = `# Gas Town HQ .gitignore
 # Explicitly track (override above patterns)
 # =============================================================================
 # Note: .beads/ has its own .gitignore that handles SQLite files
-# and keeps issues.jsonl, metadata.json, config.yaml as source of truth
+# and keeps issues.jsonl, metadata.json, config file as source of truth
 `
 
 func runGitInit(cmd *cobra.Command, args []string) error {

internal/constants/constants.go

@@ -70,9 +70,6 @@ const (
 	// FileConfigJSON is the general config file.
 	FileConfigJSON = "config.json"
 
-	// FileConfigYAML is the beads config file.
-	FileConfigYAML = "config.yaml"
-
 	// FileAccountsJSON is the accounts configuration file in mayor/.
 	FileAccountsJSON = "accounts.json"
 )

internal/doctor/branch_check.go

@@ -273,8 +273,9 @@ func (c *BeadsSyncOrphanCheck) Run(ctx *CheckContext) *CheckResult {
 		}
 		// Check if it's a code file
 		if strings.HasSuffix(f, ".go") || strings.HasSuffix(f, ".md") ||
+			strings.HasSuffix(f, ".toml") || strings.HasSuffix(f, ".json") ||
 			strings.HasSuffix(f, ".yaml") || strings.HasSuffix(f, ".yml") ||
-			strings.HasSuffix(f, ".json") || strings.HasSuffix(f, ".tmpl") {
+			strings.HasSuffix(f, ".tmpl") {
 			codeFiles = append(codeFiles, f)
 		}
 	}

internal/rig/manager.go

@@ -408,6 +408,7 @@ func (m *Manager) initAgentStates(rigPath string) error {
 // initBeads initializes the beads database at rig level.
 // The project's .beads/config.yaml determines sync-branch settings.
 // Use `bd doctor --fix` in the project to configure sync-branch if needed.
+// TODO(bd-yaml): beads config should migrate to JSON (see beads issue)
 func (m *Manager) initBeads(rigPath, prefix string) error {
 	beadsDir := filepath.Join(rigPath, ".beads")
 	if err := os.MkdirAll(beadsDir, 0755); err != nil {
@@ -419,6 +420,7 @@ func (m *Manager) initBeads(rigPath, prefix string) error {
 	cmd.Dir = rigPath
 	if err := cmd.Run(); err != nil {
 		// bd might not be installed or --no-agents not supported, create minimal structure
+		// Note: beads currently expects YAML format for config
 		configPath := filepath.Join(beadsDir, "config.yaml")
 		configContent := fmt.Sprintf("prefix: %s\n", prefix)
 		if writeErr := os.WriteFile(configPath, []byte(configContent), 0644); writeErr != nil {
@@ -747,7 +749,7 @@ This directory contains town-level plugins that run during Deacon patrol cycles.
 ## Plugin Structure
 
 Each plugin is a directory containing:
-- plugin.md - Plugin definition with YAML frontmatter
+- plugin.md - Plugin definition with TOML frontmatter
 
 ## Gate Types
 

internal/templates/roles/witness.md.tmpl

@@ -274,23 +274,16 @@ This sends handoff mail, respawns fresh. Your next instance picks up from your h
 
 Your handoff state is tracked in a pinned bead: `witness Handoff`
 
-```yaml
-# Find with: bd list | grep "witness Handoff"
-attached_molecule: mol-witness-patrol
-attached_at: 2025-12-24T10:00:00Z
-
-# Nudge escalation tracking
-nudges:
-  toast:
-    count: 2
-    last: "2025-12-24T10:30:00Z"
-  ace:
-    count: 0
-    last: null
-
-# Polecats queued for cleanup
-pending_cleanup:
-  - nux  # received POLECAT_DONE, awaiting verification
+```json
+{
+  "attached_molecule": "mol-witness-patrol",
+  "attached_at": "2025-12-24T10:00:00Z",
+  "nudges": {
+    "toast": {"count": 2, "last": "2025-12-24T10:30:00Z"},
+    "ace": {"count": 0, "last": null}
+  },
+  "pending_cleanup": ["nux"]
+}
 ```
 
 On startup, check for attached work: