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/create.go

@@ -272,6 +272,6 @@ func init() {
 	createCmd.Flags().String("external-ref", "", "External reference (e.g., 'gh-9', 'jira-ABC')")
 	createCmd.Flags().StringSlice("deps", []string{}, "Dependencies in format 'type:id' or 'id' (e.g., 'discovered-from:bd-20,blocks:bd-15' or 'bd-20')")
 	createCmd.Flags().Bool("force", false, "Force creation even if prefix doesn't match database prefix")
-	createCmd.Flags().Bool("json", false, "Output JSON format")
+	// Note: --json flag is defined as a persistent flag in main.go, not here
 	rootCmd.AddCommand(createCmd)
 }