Updated interaction between custom CLI syntax and Cobra flags

opal-task/cmd/root.go

@@ -12,9 +12,10 @@ import (
 
 // ParsedArgs represents preprocessed command arguments
 type ParsedArgs struct {
-	Command   string
-	Filters   []string
-	Modifiers []string
+	Command     string
+	Filters     []string
+	Modifiers   []string
+	CmdArgIndex int // position of command in os.Args[1:], -1 if not found
 }
 
 // Context key for parsed args
@@ -84,28 +85,29 @@ func Execute() error {
 	if len(os.Args) > 1 {
 		firstArg := os.Args[1]
 		if firstArg == "-h" || firstArg == "--help" || firstArg == "help" {
-			// Let Cobra handle help - skip preprocessing
 			return rootCmd.Execute()
 		}
 	}
 
-	// Preprocess arguments BEFORE Cobra routing
+	// Preprocess arguments (read-only scan — os.Args is never mutated)
 	if len(os.Args) > 1 {
 		parsed := preprocessArgs(os.Args[1:])
-
-		// Store in context for commands to use
 		ctx := context.WithValue(context.Background(), parsedArgsKey, parsed)
 		rootCmd.SetContext(ctx)
 
-		// Rewrite os.Args for Cobra based on parsed command
-		// This allows Cobra to route to the correct command
-		if parsed.Command != "list" || len(parsed.Filters) > 0 || len(parsed.Modifiers) > 0 {
-			// Reconstruct args: [command, ...filters, ...modifiers]
-			newArgs := []string{os.Args[0], parsed.Command}
-			newArgs = append(newArgs, parsed.Filters...)
-			newArgs = append(newArgs, parsed.Modifiers...)
-			os.Args = newArgs
+		// Build clean args for Cobra via SetArgs (os.Args stays untouched).
+		if parsed.CmdArgIndex >= 0 {
+			i := parsed.CmdArgIndex + 1            // offset for binary name in os.Args
+			cmdAndAfter := os.Args[i:]              // command + subcommands + their flags
+			preCmdFlags := collectFlags(os.Args[1:i]) // persistent flags before command
+
+			cobraArgs := make([]string, 0, len(cmdAndAfter)+len(preCmdFlags))
+			cobraArgs = append(cobraArgs, cmdAndAfter...)
+			cobraArgs = append(cobraArgs, preCmdFlags...)
+			rootCmd.SetArgs(cobraArgs)
 		}
+		// CmdArgIndex == -1: no command found, don't call SetArgs.
+		// Cobra processes os.Args naturally → root command → default report.
 	}
 
 	return rootCmd.Execute()
@@ -127,9 +129,10 @@ func getParsedArgs(cmd *cobra.Command) *ParsedArgs {
 func preprocessArgs(args []string) *ParsedArgs {
 	if len(args) == 0 {
 		return &ParsedArgs{
-			Command:   "list", // Default command
-			Filters:   []string{},
-			Modifiers: []string{},
+			Command:     "list", // Default command
+			Filters:     []string{},
+			Modifiers:   []string{},
+			CmdArgIndex: -1,
 		}
 	}
 
@@ -167,9 +170,10 @@ func preprocessArgs(args []string) *ParsedArgs {
 	// If no command found, treat as filters for default list command
 	if cmdIdx == -1 {
 		return &ParsedArgs{
-			Command:   "list",
-			Filters:   stripFlags(args),
-			Modifiers: []string{},
+			Command:     "list",
+			Filters:     stripFlags(args),
+			Modifiers:   []string{},
+			CmdArgIndex: -1,
 		}
 	}
 
@@ -183,16 +187,18 @@ func preprocessArgs(args []string) *ParsedArgs {
 	// Determine how to interpret right args
 	if commandsWithModifiers[cmdName] {
 		return &ParsedArgs{
-			Command:   cmdName,
-			Filters:   leftArgs,
-			Modifiers: rightArgs,
+			Command:     cmdName,
+			Filters:     leftArgs,
+			Modifiers:   rightArgs,
+			CmdArgIndex: cmdIdx,
 		}
 	} else {
 		allFilters := append(leftArgs, rightArgs...)
 		return &ParsedArgs{
-			Command:   cmdName,
-			Filters:   allFilters,
-			Modifiers: []string{},
+			Command:     cmdName,
+			Filters:     allFilters,
+			Modifiers:   []string{},
+			CmdArgIndex: cmdIdx,
 		}
 	}
 }
@@ -208,6 +214,35 @@ func stripFlags(args []string) []string {
 	return result
 }
 
+// collectFlags extracts flag arguments (with their values) from a slice.
+// Uses Cobra's persistent flag registry to determine if a flag takes a value.
+func collectFlags(args []string) []string {
+	var flags []string
+	for i := 0; i < len(args); i++ {
+		if !strings.HasPrefix(args[i], "-") {
+			continue
+		}
+		flags = append(flags, args[i])
+		// If flag uses = syntax, value is already included
+		if strings.Contains(args[i], "=") {
+			continue
+		}
+		// Check if this flag takes a value argument
+		if i+1 < len(args) {
+			name := strings.TrimLeft(args[i], "-")
+			f := rootCmd.PersistentFlags().Lookup(name)
+			if f == nil && len(name) == 1 {
+				f = rootCmd.PersistentFlags().ShorthandLookup(name)
+			}
+			if f != nil && f.Value.Type() != "bool" {
+				i++
+				flags = append(flags, args[i])
+			}
+		}
+	}
+	return flags
+}
+
 func init() {
 	// Add persistent flags for directory overrides
 	rootCmd.PersistentFlags().StringVar(&configDirFlag, "config-dir", "",