fix(daemon): silence deprecation warnings in --json mode

Follow-up fixes to PR #1006:
- Silence deprecation warnings when --json flag is set (agent ergonomics)
- Remove unused outputStatusJSON() function
- Remove unused encoding/json import from daemon_status.go

Agents parsing JSON output dont need deprecation warnings cluttering stderr.
The subcommand syntax (bd daemon start) remains the documented path forward.

See bd-ntl3b for deduplication work, bd-kpa7c for type consolidation.

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

cmd/bd/daemon.go

@@ -67,21 +67,23 @@ Run 'bd daemon --help' to see all subcommands.`,
 			return
 		}
 
-		// Show deprecation warnings for flag-based actions
-		if start {
-			fmt.Fprintf(os.Stderr, "Warning: --start is deprecated, use 'bd daemon start' instead\n")
-		}
-		if stop {
-			fmt.Fprintf(os.Stderr, "Warning: --stop is deprecated, use 'bd daemon stop' instead\n")
-		}
-		if stopAll {
-			fmt.Fprintf(os.Stderr, "Warning: --stop-all is deprecated, use 'bd daemon killall' instead\n")
-		}
-		if status {
-			fmt.Fprintf(os.Stderr, "Warning: --status is deprecated, use 'bd daemon status' instead\n")
-		}
-		if health {
-			fmt.Fprintf(os.Stderr, "Warning: --health is deprecated, use 'bd daemon status --all' instead\n")
+		// Show deprecation warnings for flag-based actions (skip in JSON mode for agent ergonomics)
+		if !jsonOutput {
+			if start {
+				fmt.Fprintf(os.Stderr, "Warning: --start is deprecated, use 'bd daemon start' instead\n")
+			}
+			if stop {
+				fmt.Fprintf(os.Stderr, "Warning: --stop is deprecated, use 'bd daemon stop' instead\n")
+			}
+			if stopAll {
+				fmt.Fprintf(os.Stderr, "Warning: --stop-all is deprecated, use 'bd daemon killall' instead\n")
+			}
+			if status {
+				fmt.Fprintf(os.Stderr, "Warning: --status is deprecated, use 'bd daemon status' instead\n")
+			}
+			if health {
+				fmt.Fprintf(os.Stderr, "Warning: --health is deprecated, use 'bd daemon status --all' instead\n")
+			}
 		}
 
 		// If auto-commit/auto-push flags weren't explicitly provided, read from config

cmd/bd/daemon_status.go

@@ -1,7 +1,6 @@
 package main
 
 import (
-	"encoding/json"
 	"fmt"
 	"os"
 	"path/filepath"
@@ -443,9 +442,3 @@ func showAllDaemonsStatus(cmd *cobra.Command) {
 		os.Exit(1)
 	}
 }
-
-// outputStatusJSON outputs the status as JSON (helper to avoid duplicating json.Marshal)
-func outputStatusJSON(v interface{}) {
-	data, _ := json.MarshalIndent(v, "", "  ")
-	fmt.Println(string(data))
-}