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/list.go

@@ -240,7 +240,7 @@ func init() {
 	listCmd.Flags().IntP("limit", "n", 0, "Limit results")
 	listCmd.Flags().String("format", "", "Output format: 'digraph' (for golang.org/x/tools/cmd/digraph), 'dot' (Graphviz), or Go template")
 	listCmd.Flags().Bool("all", false, "Show all issues (default behavior; flag provided for CLI familiarity)")
-	listCmd.Flags().Bool("json", false, "Output JSON format")
+	// Note: --json flag is defined as a persistent flag in main.go, not here
 	rootCmd.AddCommand(listCmd)
 }