diff --git a/scripts/bootstrap.py b/scripts/bootstrap.py
index 3302322..a92d85a 100644
--- a/scripts/bootstrap.py
+++ b/scripts/bootstrap.py
@@ -939,6 +939,19 @@ def main() -> int:
         # Install the project into the local venv (editable mode is the default, opinionated)
         if not args.quiet:
             print("Installing project into local venv (editable mode)")
+        
+        # Clean up old pip-generated entry point wrapper to avoid stale references
+        import platform
+        if platform.system() != "Windows":
+            old_mm = venv_dir / "bin" / "mm"
+            if old_mm.exists():
+                try:
+                    old_mm.unlink()
+                    if not args.quiet:
+                        print(f"Removed old entry point wrapper: {old_mm}")
+                except Exception:
+                    pass
+        
         run([str(venv_python), "-m", "pip", "install", "--no-cache-dir", "-e", str(repo_root / "scripts")])
 
         # Verify top-level 'CLI' import and, if missing, attempt to make it available
@@ -1200,6 +1213,13 @@ if (Test-Path (Join-Path $repo 'CLI.py')) {
                     user_bin.mkdir(parents=True, exist_ok=True)
 
                     mm_sh = user_bin / "mm"
+                    
+                    # Remove old launcher to overwrite with new one
+                    if mm_sh.exists():
+                        try:
+                            mm_sh.unlink()
+                        except Exception:
+                            pass
                     sh_text = (
                         "#!/usr/bin/env bash\n"
                         "set -e\n"