diff --git a/.github/workflows/github-remote-mcp-auth-test.lock.yml b/.github/workflows/github-remote-mcp-auth-test.lock.yml
index e68e97abe7..66e01c53b9 100644
--- a/.github/workflows/github-remote-mcp-auth-test.lock.yml
+++ b/.github/workflows/github-remote-mcp-auth-test.lock.yml
@@ -396,6 +396,11 @@ jobs:
                   "X-MCP-Readonly": "true",
                   "X-MCP-Toolsets": "repos,issues,discussions"
                 },
+                "tools": [
+                  "get_repository",
+                  "list_issues",
+                  "issue_read"
+                ],
                 "env": {
                   "GITHUB_PERSONAL_ACCESS_TOKEN": "\${GITHUB_MCP_SERVER_TOKEN}"
                 }
diff --git a/pkg/cli/file_tracker.go b/pkg/cli/file_tracker.go
index aa8de2899f..41c89d3cd8 100644
--- a/pkg/cli/file_tracker.go
+++ b/pkg/cli/file_tracker.go
@@ -7,6 +7,7 @@ import (
 	"path/filepath"
 	"strings"
 
+	"github.com/githubnext/gh-aw/pkg/console"
 	"github.com/githubnext/gh-aw/pkg/logger"
 )
 
@@ -161,7 +162,7 @@ func (ft *FileTracker) RollbackModifiedFiles(verbose bool) error {
 			}
 		} else {
 			if verbose {
-				fmt.Printf("    Warning: No original content stored for %s\n", file)
+				fmt.Fprintln(os.Stderr, console.FormatWarningMessage(fmt.Sprintf("No original content stored for %s", file)))
 			}
 		}
 	}
diff --git a/pkg/cli/run_workflow_tracking.go b/pkg/cli/run_workflow_tracking.go
index 78bebcedda..f16065b847 100644
--- a/pkg/cli/run_workflow_tracking.go
+++ b/pkg/cli/run_workflow_tracking.go
@@ -3,6 +3,7 @@ package cli
 import (
 	"encoding/json"
 	"fmt"
+	"os"
 	"os/exec"
 	"time"
 
@@ -83,7 +84,7 @@ func getLatestWorkflowRunWithRetry(lockFileName string, repo string, verbose boo
 		if err != nil {
 			lastErr = fmt.Errorf("failed to get workflow runs: %w", err)
 			if verbose {
-				fmt.Printf("Attempt %d/%d failed: %v\n", attempt+1, maxRetries, err)
+				fmt.Fprintln(os.Stderr, console.FormatErrorMessage(fmt.Sprintf("Attempt %d/%d failed: %v", attempt+1, maxRetries, err)))
 			}
 			continue
 		}
@@ -108,7 +109,7 @@ func getLatestWorkflowRunWithRetry(lockFileName string, repo string, verbose boo
 		if err := json.Unmarshal(output, &runs); err != nil {
 			lastErr = fmt.Errorf("failed to parse workflow run data: %w", err)
 			if verbose {
-				fmt.Printf("Attempt %d/%d failed to parse JSON: %v\n", attempt+1, maxRetries, err)
+				fmt.Fprintln(os.Stderr, console.FormatErrorMessage(fmt.Sprintf("Attempt %d/%d failed to parse JSON: %v", attempt+1, maxRetries, err)))
 			}
 			continue
 		}
@@ -129,7 +130,7 @@ func getLatestWorkflowRunWithRetry(lockFileName string, repo string, verbose boo
 			if parsedTime, err := time.Parse(time.RFC3339, run.CreatedAt); err == nil {
 				createdAt = parsedTime
 			} else if verbose {
-				fmt.Printf("Warning: Could not parse creation time '%s': %v\n", run.CreatedAt, err)
+				fmt.Fprintln(os.Stderr, console.FormatWarningMessage(fmt.Sprintf("Could not parse creation time '%s': %v", run.CreatedAt, err)))
 			}
 		}