feat: Add 'bd orphans' command with DRY refactoring of orphan detection

Implements the 'bd orphans' command to identify issues referenced in commits
but still open in the database, and refactors to eliminate code duplication.

- Creates cmd/bd/orphans.go with Cobra command structure
- Identifies orphaned issues (referenced in git commits but still open/in_progress)
- Supports multiple output formats (human, JSON, detailed)
- Auto-close with --fix flag

DRY refactoring:
- Extracted FindOrphanedIssues() to cmd/bd/doctor/git.go as shared core logic
- Moved OrphanIssue type to cmd/bd/doctor/types.go
- Refactored CheckOrphanedIssues() to use FindOrphanedIssues()

Cherry-picked from PR #767

Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/orphans.go

@@ -0,0 +1,129 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"os/exec"
+	"sort"
+	"strings"
+
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/cmd/bd/doctor"
+	"github.com/steveyegge/beads/internal/ui"
+)
+
+var orphansCmd = &cobra.Command{
+	Use:   "orphans",
+	Short: "Identify orphaned issues (referenced in commits but still open)",
+	Long: `Identify orphaned issues - issues that are referenced in commit messages but remain open or in_progress in the database.
+
+This helps identify work that has been implemented but not formally closed.
+
+Examples:
+  bd orphans              # Show orphaned issues
+  bd orphans --json       # Machine-readable output
+  bd orphans --details    # Show full commit information
+  bd orphans --fix        # Close orphaned issues with confirmation`,
+	Run: func(cmd *cobra.Command, args []string) {
+		path := "."
+		orphans, err := findOrphanedIssues(path)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+			os.Exit(1)
+		}
+
+		fix, _ := cmd.Flags().GetBool("fix")
+		details, _ := cmd.Flags().GetBool("details")
+
+		if jsonOutput {
+			outputJSON(orphans)
+			return
+		}
+
+		if len(orphans) == 0 {
+			fmt.Printf("%s No orphaned issues found\n", ui.RenderPass("✓"))
+			return
+		}
+
+		fmt.Printf("\n%s Found %d orphaned issue(s):\n\n", ui.RenderWarn("⚠"), len(orphans))
+
+		// Sort by issue ID for consistent output
+		sort.Slice(orphans, func(i, j int) bool {
+			return orphans[i].IssueID < orphans[j].IssueID
+		})
+
+		for i, orphan := range orphans {
+			fmt.Printf("%d. %s: %s\n", i+1, ui.RenderID(orphan.IssueID), orphan.Title)
+			fmt.Printf("   Status: %s\n", orphan.Status)
+			if details && orphan.LatestCommit != "" {
+				fmt.Printf("   Latest commit: %s - %s\n", orphan.LatestCommit, orphan.LatestCommitMessage)
+			}
+		}
+
+		if fix {
+			fmt.Println()
+			fmt.Printf("This will close %d orphaned issue(s). Continue? (Y/n): ", len(orphans))
+			var response string
+			fmt.Scanln(&response)
+			response = strings.ToLower(strings.TrimSpace(response))
+			if response != "" && response != "y" && response != "yes" {
+				fmt.Println("Canceled.")
+				return
+			}
+
+			// Close orphaned issues
+			closedCount := 0
+			for _, orphan := range orphans {
+				err := closeIssue(orphan.IssueID)
+				if err != nil {
+					fmt.Fprintf(os.Stderr, "Error closing %s: %v\n", orphan.IssueID, err)
+				} else {
+					fmt.Printf("✓ Closed %s\n", orphan.IssueID)
+					closedCount++
+				}
+			}
+			fmt.Printf("\nClosed %d issue(s)\n", closedCount)
+		}
+	},
+}
+
+// orphanIssueOutput is the JSON output format for orphaned issues
+type orphanIssueOutput struct {
+	IssueID              string `json:"issue_id"`
+	Title                string `json:"title"`
+	Status               string `json:"status"`
+	LatestCommit         string `json:"latest_commit,omitempty"`
+	LatestCommitMessage  string `json:"latest_commit_message,omitempty"`
+}
+
+// findOrphanedIssues wraps the shared doctor package function and converts to output format
+func findOrphanedIssues(path string) ([]orphanIssueOutput, error) {
+	orphans, err := doctor.FindOrphanedIssues(path)
+	if err != nil {
+		return nil, fmt.Errorf("unable to find orphaned issues: %w", err)
+	}
+
+	var output []orphanIssueOutput
+	for _, orphan := range orphans {
+		output = append(output, orphanIssueOutput{
+			IssueID:             orphan.IssueID,
+			Title:               orphan.Title,
+			Status:              orphan.Status,
+			LatestCommit:        orphan.LatestCommit,
+			LatestCommitMessage: orphan.LatestCommitMessage,
+		})
+	}
+	return output, nil
+}
+
+// closeIssue closes an issue using bd close
+func closeIssue(issueID string) error {
+	cmd := exec.Command("bd", "close", issueID, "--reason", "Implemented")
+	return cmd.Run()
+}
+
+func init() {
+	orphansCmd.Flags().BoolP("fix", "f", false, "Close orphaned issues with confirmation")
+	orphansCmd.Flags().Bool("details", false, "Show full commit information")
+	rootCmd.AddCommand(orphansCmd)
+}