cmd: Fix paths when using an env file (#4296)

* core: Fix paths when using an env file

* refactor: move path logic to loadFromEnv

cmd/main.go

@@ -361,6 +361,11 @@ func loadEnvFromFile(envFile string) error {
 		}
 	}
 
+	// Update the storage paths to ensure they have the proper
+	// value after loading a specified env file.
+	caddy.ConfigAutosavePath = filepath.Join(caddy.AppConfigDir(), "autosave.json")
+	caddy.DefaultStorage = &certmagic.FileStorage{Path: caddy.AppDataDir()}
+
 	return nil
 }