test: add e2e test suite and fix namespace/mention/assignee flags

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

cmd/root.go

@@ -44,22 +44,38 @@ func registerAliasCommands() {
 				acmd = strings.ReplaceAll(acmd, "$me", cfg.GetUser())
 				parts := strings.Fields(acmd)
 				var expanded []string
+				usedArgs := make([]bool, len(args))
 				for _, part := range parts {
 					if part == "$@" {
 						expanded = append(expanded, args...)
+						for i := range usedArgs {
+							usedArgs[i] = true
+						}
 						continue
 					}
 					hasCatchAll := strings.Contains(part, "$@")
 					replaced := part
 					if hasCatchAll {
 						replaced = strings.ReplaceAll(replaced, "$@", strings.Join(args, " "))
+						for i := range usedArgs {
+							usedArgs[i] = true
+						}
 					}
 					for i := len(args) - 1; i >= 0; i-- {
 						placeholder := fmt.Sprintf("$%d", i+1)
-						replaced = strings.ReplaceAll(replaced, placeholder, args[i])
+						if strings.Contains(replaced, placeholder) {
+							replaced = strings.ReplaceAll(replaced, placeholder, args[i])
+							usedArgs[i] = true
+						}
 					}
 					expanded = append(expanded, replaced)
 				}
+				// Forward any unconsumed args (e.g. --json flag).
+				for i, arg := range args {
+					if !usedArgs[i] {
+						expanded = append(expanded, arg)
+					}
+				}
 				rootCmd.SetArgs(expanded)
 				if err := rootCmd.Execute(); err != nil {
 					os.Exit(1)