Fix --json flag shadowing issue causing test failures

Fixed TestHashIDs_IdenticalContentDedup test failure by removing duplicate
--json flag definitions that were shadowing the global persistent flag.

Root cause: Commands had both a persistent --json flag (main.go) and local
--json flags (in individual command files). The local flags shadowed the
persistent flag, preventing jsonOutput variable from being set correctly.

Changes:
- Removed 31 duplicate --json flag definitions from 15 command files
- All commands now use the single persistent --json flag from main.go
- Commands now correctly output JSON when --json flag is specified

Test results:
- TestHashIDs_IdenticalContentDedup: Now passes (was failing)
- TestHashIDs_MultiCloneConverge: Passes without JSON parsing warnings
- All other tests: Pass with no regressions

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

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

cmd/bd/reopen.go

@@ -1,31 +1,25 @@
 package main
-
 import (
 	"context"
 	"encoding/json"
 	"fmt"
 	"os"
-
 	"github.com/fatih/color"
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/types"
 	"github.com/steveyegge/beads/internal/utils"
 )
-
 var reopenCmd = &cobra.Command{
 	Use:   "reopen [id...]",
 	Short: "Reopen one or more closed issues",
 	Long: `Reopen closed issues by setting status to 'open' and clearing the closed_at timestamp.
-
 This is more explicit than 'bd update --status open' and emits a Reopened event.`,
 	Args: cobra.MinimumNArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		reason, _ := cmd.Flags().GetString("reason")
 		// Use global jsonOutput set by PersistentPreRun
-
 		ctx := context.Background()
-		
 		// Resolve partial IDs first
 		var resolvedIDs []string
 		if daemonClient != nil {
@@ -46,9 +40,7 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 				os.Exit(1)
 			}
 		}
-		
 		reopenedIssues := []*types.Issue{}
-		
 		// If daemon is running, use RPC
 		if daemonClient != nil {
 			for _, id := range resolvedIDs {
@@ -57,18 +49,15 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 					ID:     id,
 					Status: &openStatus,
 				}
-				
 				resp, err := daemonClient.Update(updateArgs)
 				if err != nil {
 					fmt.Fprintf(os.Stderr, "Error reopening %s: %v\n", id, err)
 					continue
 				}
-				
 				// TODO: Add reason as a comment once RPC supports AddComment
 				if reason != "" {
 					fmt.Fprintf(os.Stderr, "Warning: reason not supported in daemon mode yet\n")
 				}
-				
 				if jsonOutput {
 					var issue types.Issue
 					if err := json.Unmarshal(resp.Data, &issue); err == nil {
@@ -83,26 +72,22 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 					fmt.Printf("%s Reopened %s%s\n", blue("↻"), id, reasonMsg)
 				}
 			}
-			
 			if jsonOutput && len(reopenedIssues) > 0 {
 				outputJSON(reopenedIssues)
 			}
 			return
 		}
-		
 		// Fall back to direct storage access
 		if store == nil {
 			fmt.Fprintln(os.Stderr, "Error: database not initialized")
 			os.Exit(1)
 		}
-		
 		for _, id := range args {
 			fullID, err := utils.ResolvePartialID(ctx, store, id)
 			if err != nil {
 				fmt.Fprintf(os.Stderr, "Error resolving %s: %v\n", id, err)
 				continue
 			}
-			
 			// UpdateIssue automatically clears closed_at when status changes from closed
 			updates := map[string]interface{}{
 				"status": string(types.StatusOpen),
@@ -111,14 +96,12 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 				fmt.Fprintf(os.Stderr, "Error reopening %s: %v\n", fullID, err)
 				continue
 			}
-
 			// Add reason as a comment if provided
 			if reason != "" {
 				if err := store.AddComment(ctx, fullID, actor, reason); err != nil {
 					fmt.Fprintf(os.Stderr, "Warning: failed to add comment to %s: %v\n", fullID, err)
 				}
 			}
-
 			if jsonOutput {
 				issue, _ := store.GetIssue(ctx, fullID)
 				if issue != nil {
@@ -133,20 +116,16 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 				fmt.Printf("%s Reopened %s%s\n", blue("↻"), fullID, reasonMsg)
 			}
 		}
-
 		// Schedule auto-flush if any issues were reopened
 		if len(args) > 0 {
 			markDirtyAndScheduleFlush()
 		}
-
 		if jsonOutput && len(reopenedIssues) > 0 {
 			outputJSON(reopenedIssues)
 		}
 	},
 }
-
 func init() {
 	reopenCmd.Flags().StringP("reason", "r", "", "Reason for reopening")
-	reopenCmd.Flags().Bool("json", false, "Output JSON format")
 	rootCmd.AddCommand(reopenCmd)
 }