refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"

Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go

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

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

cmd/bd/formula.go

@@ -1,12 +1,15 @@
 package main
 
 import (
+	"bytes"
+	"encoding/json"
 	"fmt"
 	"os"
 	"path/filepath"
 	"sort"
 	"strings"
 
+	"github.com/BurntSushi/toml"
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/formula"
 	"github.com/steveyegge/beads/internal/ui"
@@ -18,8 +21,8 @@ var formulaCmd = &cobra.Command{
 	Short: "Manage workflow formulas",
 	Long: `Manage workflow formulas - the source layer for molecule templates.
 
-Formulas are JSON files (.formula.json) that define workflows with composition rules.
-They are "cooked" into ephemeral protos which can then be poured or wisped.
+Formulas are YAML/JSON files that define workflows with composition rules.
+They are "cooked" into proto beads which can then be poured or wisped.
 
 The Rig → Cook → Run lifecycle:
   - Rig: Compose formulas (extends, compose)
@@ -363,7 +366,7 @@ func getFormulaSearchPaths() []string {
 	return paths
 }
 
-// scanFormulaDir scans a directory for formula files.
+// scanFormulaDir scans a directory for formula files (both TOML and JSON).
 func scanFormulaDir(dir string) ([]*formula.Formula, error) {
 	entries, err := os.ReadDir(dir)
 	if err != nil {
@@ -377,11 +380,13 @@ func scanFormulaDir(dir string) ([]*formula.Formula, error) {
 		if entry.IsDir() {
 			continue
 		}
-		if !strings.HasSuffix(entry.Name(), formula.FormulaExt) {
+		// Support both .formula.toml and .formula.json
+		name := entry.Name()
+		if !strings.HasSuffix(name, formula.FormulaExtTOML) && !strings.HasSuffix(name, formula.FormulaExtJSON) {
 			continue
 		}
 
-		path := filepath.Join(dir, entry.Name())
+		path := filepath.Join(dir, name)
 		f, err := parser.ParseFile(path)
 		if err != nil {
 			continue // Skip invalid formulas
@@ -471,10 +476,297 @@ func printFormulaStepsTree(steps []*formula.Step, indent string) {
 	}
 }
 
+// formulaConvertCmd converts JSON formulas to TOML.
+var formulaConvertCmd = &cobra.Command{
+	Use:   "convert <formula-name|path> [--all]",
+	Short: "Convert formula from JSON to TOML",
+	Long: `Convert formula files from JSON to TOML format.
+
+TOML format provides better ergonomics:
+  - Multi-line strings without \n escaping
+  - Human-readable diffs
+  - Comments allowed
+
+The convert command reads a .formula.json file and outputs .formula.toml.
+The original JSON file is preserved (use --delete to remove it).
+
+Examples:
+  bd formula convert shiny              # Convert shiny.formula.json to .toml
+  bd formula convert ./my.formula.json  # Convert specific file
+  bd formula convert --all              # Convert all JSON formulas
+  bd formula convert shiny --delete     # Convert and remove JSON file
+  bd formula convert shiny --stdout     # Print TOML to stdout`,
+	Run: runFormulaConvert,
+}
+
+var (
+	convertAll    bool
+	convertDelete bool
+	convertStdout bool
+)
+
+func runFormulaConvert(cmd *cobra.Command, args []string) {
+	if convertAll {
+		convertAllFormulas()
+		return
+	}
+
+	if len(args) == 0 {
+		fmt.Fprintf(os.Stderr, "Error: formula name or path required\n")
+		fmt.Fprintf(os.Stderr, "Usage: bd formula convert <name|path> [--all]\n")
+		os.Exit(1)
+	}
+
+	name := args[0]
+
+	// Determine the JSON file path
+	var jsonPath string
+	if strings.HasSuffix(name, formula.FormulaExtJSON) {
+		// Direct path provided
+		jsonPath = name
+	} else if strings.HasSuffix(name, formula.FormulaExtTOML) {
+		fmt.Fprintf(os.Stderr, "Error: %s is already a TOML file\n", name)
+		os.Exit(1)
+	} else {
+		// Search for the formula in search paths
+		jsonPath = findFormulaJSON(name)
+		if jsonPath == "" {
+			fmt.Fprintf(os.Stderr, "Error: JSON formula %q not found\n", name)
+			fmt.Fprintf(os.Stderr, "\nSearch paths:\n")
+			for _, p := range getFormulaSearchPaths() {
+				fmt.Fprintf(os.Stderr, "  %s\n", p)
+			}
+			os.Exit(1)
+		}
+	}
+
+	// Parse the JSON file
+	parser := formula.NewParser()
+	f, err := parser.ParseFile(jsonPath)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error parsing %s: %v\n", jsonPath, err)
+		os.Exit(1)
+	}
+
+	// Convert to TOML
+	tomlData, err := formulaToTOML(f)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error converting to TOML: %v\n", err)
+		os.Exit(1)
+	}
+
+	if convertStdout {
+		fmt.Print(string(tomlData))
+		return
+	}
+
+	// Determine output path
+	tomlPath := strings.TrimSuffix(jsonPath, formula.FormulaExtJSON) + formula.FormulaExtTOML
+
+	// Write the TOML file
+	if err := os.WriteFile(tomlPath, tomlData, 0600); err != nil {
+		fmt.Fprintf(os.Stderr, "Error writing %s: %v\n", tomlPath, err)
+		os.Exit(1)
+	}
+
+	fmt.Printf("✓ Converted: %s\n", tomlPath)
+
+	if convertDelete {
+		if err := os.Remove(jsonPath); err != nil {
+			fmt.Fprintf(os.Stderr, "Warning: could not delete %s: %v\n", jsonPath, err)
+		} else {
+			fmt.Printf("✓ Deleted: %s\n", jsonPath)
+		}
+	}
+}
+
+func convertAllFormulas() {
+	converted := 0
+	errors := 0
+
+	for _, dir := range getFormulaSearchPaths() {
+		entries, err := os.ReadDir(dir)
+		if err != nil {
+			continue
+		}
+
+		parser := formula.NewParser(dir)
+
+		for _, entry := range entries {
+			if entry.IsDir() {
+				continue
+			}
+			if !strings.HasSuffix(entry.Name(), formula.FormulaExtJSON) {
+				continue
+			}
+
+			jsonPath := filepath.Join(dir, entry.Name())
+			tomlPath := strings.TrimSuffix(jsonPath, formula.FormulaExtJSON) + formula.FormulaExtTOML
+
+			// Skip if TOML already exists
+			if _, err := os.Stat(tomlPath); err == nil {
+				fmt.Printf("⏭ Skipped (TOML exists): %s\n", entry.Name())
+				continue
+			}
+
+			f, err := parser.ParseFile(jsonPath)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "✗ Error parsing %s: %v\n", jsonPath, err)
+				errors++
+				continue
+			}
+
+			tomlData, err := formulaToTOML(f)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "✗ Error converting %s: %v\n", jsonPath, err)
+				errors++
+				continue
+			}
+
+			if err := os.WriteFile(tomlPath, tomlData, 0600); err != nil {
+				fmt.Fprintf(os.Stderr, "✗ Error writing %s: %v\n", tomlPath, err)
+				errors++
+				continue
+			}
+
+			fmt.Printf("✓ Converted: %s\n", tomlPath)
+			converted++
+
+			if convertDelete {
+				if err := os.Remove(jsonPath); err != nil {
+					fmt.Fprintf(os.Stderr, "Warning: could not delete %s: %v\n", jsonPath, err)
+				}
+			}
+		}
+	}
+
+	fmt.Printf("\nConverted %d formulas", converted)
+	if errors > 0 {
+		fmt.Printf(" (%d errors)", errors)
+	}
+	fmt.Println()
+}
+
+// findFormulaJSON searches for a JSON formula file by name.
+func findFormulaJSON(name string) string {
+	for _, dir := range getFormulaSearchPaths() {
+		path := filepath.Join(dir, name+formula.FormulaExtJSON)
+		if _, err := os.Stat(path); err == nil {
+			return path
+		}
+	}
+	return ""
+}
+
+// formulaToTOML converts a Formula to TOML bytes.
+// Uses a custom structure optimized for TOML readability.
+func formulaToTOML(f *formula.Formula) ([]byte, error) {
+	// We need to re-read the original JSON to get the raw structure
+	// because the Formula struct loses some ordering/formatting
+	if f.Source == "" {
+		return nil, fmt.Errorf("formula has no source path")
+	}
+
+	// Read the original JSON
+	jsonData, err := os.ReadFile(f.Source)
+	if err != nil {
+		return nil, fmt.Errorf("reading source: %w", err)
+	}
+
+	// Parse into a map to preserve structure
+	var raw map[string]interface{}
+	if err := json.Unmarshal(jsonData, &raw); err != nil {
+		return nil, fmt.Errorf("parsing JSON: %w", err)
+	}
+
+	// Fix float64 to int for known integer fields
+	fixIntegerFields(raw)
+
+	// Encode to TOML
+	var buf bytes.Buffer
+	encoder := toml.NewEncoder(&buf)
+	encoder.Indent = ""
+	if err := encoder.Encode(raw); err != nil {
+		return nil, fmt.Errorf("encoding TOML: %w", err)
+	}
+
+	// Post-process to convert escaped \n in strings to multi-line strings
+	result := convertToMultiLineStrings(buf.String())
+
+	return []byte(result), nil
+}
+
+// convertToMultiLineStrings post-processes TOML to use multi-line strings
+// where strings contain newlines. This improves readability for descriptions.
+func convertToMultiLineStrings(input string) string {
+	// Regular expression to match key = "value with \n"
+	// We look for description fields specifically as those benefit most
+	lines := strings.Split(input, "\n")
+	var result []string
+
+	for _, line := range lines {
+		// Check if this line has a string with escaped newlines
+		if strings.Contains(line, "\\n") {
+			// Find the key = "..." pattern
+			eqIdx := strings.Index(line, " = \"")
+			if eqIdx > 0 && strings.HasSuffix(line, "\"") {
+				key := strings.TrimSpace(line[:eqIdx])
+				// Only convert description fields
+				if key == "description" {
+					// Extract the value (without quotes)
+					value := line[eqIdx+4 : len(line)-1]
+					// Unescape the newlines
+					value = strings.ReplaceAll(value, "\\n", "\n")
+					// Use multi-line string syntax
+					result = append(result, fmt.Sprintf("%s = \"\"\"\n%s\"\"\"", key, value))
+					continue
+				}
+			}
+		}
+		result = append(result, line)
+	}
+
+	return strings.Join(result, "\n")
+}
+
+// fixIntegerFields recursively fixes float64 values that should be integers.
+// JSON unmarshals all numbers as float64, but TOML needs proper int types.
+func fixIntegerFields(m map[string]interface{}) {
+	// Known integer fields
+	intFields := map[string]bool{
+		"version":  true,
+		"priority": true,
+		"count":    true,
+		"max":      true,
+	}
+
+	for k, v := range m {
+		switch val := v.(type) {
+		case float64:
+			// Convert whole numbers to int64 if they're known int fields
+			if intFields[k] && val == float64(int64(val)) {
+				m[k] = int64(val)
+			}
+		case map[string]interface{}:
+			fixIntegerFields(val)
+		case []interface{}:
+			for _, item := range val {
+				if subMap, ok := item.(map[string]interface{}); ok {
+					fixIntegerFields(subMap)
+				}
+			}
+		}
+	}
+}
+
 func init() {
 	formulaListCmd.Flags().String("type", "", "Filter by type (workflow, expansion, aspect)")
+	formulaConvertCmd.Flags().BoolVar(&convertAll, "all", false, "Convert all JSON formulas")
+	formulaConvertCmd.Flags().BoolVar(&convertDelete, "delete", false, "Delete JSON file after conversion")
+	formulaConvertCmd.Flags().BoolVar(&convertStdout, "stdout", false, "Print TOML to stdout instead of file")
 
 	formulaCmd.AddCommand(formulaListCmd)
 	formulaCmd.AddCommand(formulaShowCmd)
+	formulaCmd.AddCommand(formulaConvertCmd)
 	rootCmd.AddCommand(formulaCmd)
 }