fix(stderr): route diagnostics to stderr, keep stdout for data

`vers run --json` previously emitted 'Warning: vers.toml not found...' to
stdout, contaminating the JSON output and breaking `vers run --json | jq`.
Same shape elsewhere \u2014 six diagnostics across runconfig, presenters, and
handlers were using `fmt.Println`/`Printf` (stdout) instead of stderr.

Fixed:
- internal/runconfig/config.go      'vers.toml not found' warning
- internal/presenters/run_presenter.go      '.vers directory not found' warning
- internal/presenters/branch_presenter.go   'no VM IDs returned' error + HEAD update warning
- internal/handlers/upgrade.go      'skipping checksum verification' warning
- internal/handlers/kill.go         'about to delete VM' confirmation header

After this, `vers run --json 2>/dev/null` produces clean JSON that
`jq` can parse. Addresses agent-native CLI principle 2 (data on stdout,
diagnostics on stderr).

Author: AlephNotation

internal/handlers/kill.go

@@ -3,6 +3,7 @@ package handlers
 import (
 	"context"
 	"fmt"
+	"os"
 
 	"github.com/hdresearch/vers-cli/internal/app"
 	"github.com/hdresearch/vers-cli/internal/presenters"
@@ -30,7 +31,7 @@ func HandleKill(ctx context.Context, a *app.App, r KillReq) error {
 	// Confirm if needed
 	if !r.SkipConfirmation {
 		for _, t := range targets {
-			fmt.Printf("Warning: You are about to delete VM '%s'\n", t)
+			fmt.Fprintf(os.Stderr, "Warning: You are about to delete VM '%s'\n", t)
 		}
 		ok, _ := a.Prompter.YesNo("Proceed")
 		if !ok {

internal/handlers/upgrade.go

@@ -107,7 +107,7 @@ func performUpgrade(DebugPrint func(string, ...any), release *update.GitHubRelea
 		}
 		fmt.Println("Checksum verification passed")
 	} else if skipChecksum {
-		fmt.Println("warning: skipping checksum verification (not recommended)")
+		fmt.Fprintln(os.Stderr, "warning: skipping checksum verification (not recommended)")
 	}
 
 	currentExe, err := os.Executable()

internal/presenters/branch_presenter.go

@@ -2,6 +2,7 @@ package presenters
 
 import (
 	"fmt"
+	"os"
 
 	"github.com/hdresearch/vers-cli/internal/app"
 )
@@ -12,7 +13,7 @@ func RenderBranch(a *app.App, res BranchView) {
 		newIDs = []string{res.NewID}
 	}
 	if len(newIDs) == 0 {
-		fmt.Println("Error: no VM IDs returned from branch operation")
+		fmt.Fprintln(os.Stderr, "Error: no VM IDs returned from branch operation")
 		return
 	}
 	numNew := len(newIDs)
@@ -50,7 +51,7 @@ func RenderBranch(a *app.App, res BranchView) {
 	}
 
 	if res.CheckoutErr != nil {
-		fmt.Printf("WARNING: Failed to update HEAD: %v\n", res.CheckoutErr)
+		fmt.Fprintf(os.Stderr, "WARNING: Failed to update HEAD: %v\n", res.CheckoutErr)
 		return
 	}
 

internal/presenters/run_presenter.go

@@ -2,6 +2,7 @@ package presenters
 
 import (
 	"fmt"
+	"os"
 
 	"github.com/hdresearch/vers-cli/internal/app"
 )
@@ -18,6 +19,6 @@ func RenderRun(a *app.App, v RunView) {
 	if v.HeadTarget != "" {
 		fmt.Printf("HEAD now points to: %s\n", v.HeadTarget)
 	} else {
-		fmt.Println("Warning: .vers directory not found. Run 'vers init' first.")
+		fmt.Fprintln(os.Stderr, "Warning: .vers directory not found. Run 'vers init' first.")
 	}
 }

internal/runconfig/config.go

@@ -55,7 +55,7 @@ func Default() *Config {
 func Load() (*Config, error) {
 	cfg := Default()
 	if _, err := os.Stat("vers.toml"); os.IsNotExist(err) {
-		fmt.Println("Warning: vers.toml not found, using default configuration")
+		fmt.Fprintln(os.Stderr, "Warning: vers.toml not found, using default configuration")
 		return cfg, nil
 	}
 	if _, err := toml.DecodeFile("vers.toml", cfg); err != nil {