fix: improve CLI flags and output formatting consistency

cmd/describe_stacks.go

@@ -102,9 +102,9 @@ var describeStacksCmd = &cobra.Command{
 
 func init() {
 	describeStacksCmd.DisableFlagParsing = false
-	describeStacksCmd.PersistentFlags().StringP("stack", "s", "", "Filter by a specific stack")
-	describeStacksCmd.PersistentFlags().String("json", "", "Comma-separated list of fields to include in JSON output")
-	describeStacksCmd.PersistentFlags().String("jq", "", "JQ query to transform JSON output (requires --json)")
-	describeStacksCmd.PersistentFlags().String("template", "", "Go template to format JSON output (requires --json)")
+	describeStacksCmd.Flags().StringP("stack", "s", "", "Filter by a specific stack")
+	describeStacksCmd.Flags().String("json", "", "Comma-separated list of fields to include in JSON output")
+	describeStacksCmd.Flags().String("jq", "", "JQ query to transform JSON output (requires --json)")
+	describeStacksCmd.Flags().String("template", "", "Go template to format JSON output (requires --json)")
 	describeCmd.AddCommand(describeStacksCmd)
 }

cmd/root.go

@@ -184,8 +184,6 @@ func init() {
 
 	RootCmd.PersistentFlags().String("logs-level", "Info", "Logs level. Supported log levels are Trace, Debug, Info, Warning, Off. If the log level is set to Off, Atmos will not log any messages")
 	RootCmd.PersistentFlags().String("logs-file", "/dev/stdout", "The file to write Atmos logs to. Logs can be written to any file or any standard file descriptor, including '/dev/stdout', '/dev/stderr' and '/dev/null'")
-	RootCmd.PersistentFlags().String("jq", "", "JQ query to transform the output (e.g. '.[] | {name: .name}')")
-	RootCmd.PersistentFlags().String("template", "", "Go template to format the output (supports Go templates, Sprig functions, and additional helpers)")
 
 	// Set custom usage template
 	err := templates.SetCustomUsageFunc(RootCmd)

internal/exec/format_stacks.go

@@ -26,7 +26,11 @@ func FormatStacksOutput(stacksMap map[string]any, jsonFields string, jqQuery str
 		// Use HighlightCodeWithConfig for YAML output
 		highlighted, err := u.HighlightCodeWithConfig(string(yamlBytes), atmosConfig, "yaml")
 		if err != nil {
-			return string(yamlBytes), nil
+			return string(yamlBytes) + "\n", nil
+		}
+		// For YAML output, preserve the original formatting including newlines
+		if !strings.HasSuffix(highlighted, "\n\n") {
+			highlighted += "\n"
 		}
 		return highlighted, nil
 	}
@@ -75,9 +79,10 @@ func FormatStacksOutput(stacksMap map[string]any, jsonFields string, jqQuery str
 	// Use HighlightCodeWithConfig for JSON output
 	highlighted, err := u.HighlightCodeWithConfig(string(jsonBytes), atmosConfig, "json")
 	if err != nil {
-		return string(jsonBytes), nil
+		return string(jsonBytes) + "\n", nil
 	}
-	return highlighted, nil
+	// For JSON output, ensure exactly one newline at the end
+	return strings.TrimRight(highlighted, "\n") + "\n", nil
 }
 
 // filterFields filters the input data to only include specified fields