Move legacy layout warning logic to runMigrations

Goal here is separation of concerns

src/pkg/packager/migrate.go

@@ -9,6 +9,11 @@ import "github.com/defenseunicorns/zarf/src/pkg/packager/deprecated"
 func (p *Packager) runMigrations() {
 	var warnings []string
 
+	if p.layout.IsLegacyLayout() {
+		warning := "Detected deprecated package layout, migrating to new layout - support for this package will be dropped in v1.0.0"
+		p.warnings = append(p.warnings, warning)
+	}
+
 	if len(p.cfg.Pkg.Build.Migrations) > 0 {
 		for idx, component := range p.cfg.Pkg.Components {
 			// Handle component configuration deprecations

src/pkg/packager/yaml.go

@@ -21,14 +21,7 @@ func (p *Packager) readZarfYAML(path string) error {
 	if err := utils.ReadYaml(path, &p.cfg.Pkg); err != nil {
 		return err
 	}
-
-	if p.layout.IsLegacyLayout() {
-		warning := "Detected deprecated package layout, migrating to new layout - support for this package will be dropped in v1.0.0"
-		p.warnings = append(p.warnings, warning)
-	}
-
 	p.arch = config.GetArch(p.cfg.Pkg.Metadata.Architecture, p.cfg.Pkg.Build.Architecture)
-
 	return nil
 }