add text "(non-node_modules code only)"

Co-authored-by: René <contact.9a5d6388@renegade334.me.uk>

Author: MikeMcC399

doc/api/deprecations.md

@@ -946,7 +946,7 @@ changes:
     description: Documentation-only deprecation.
 -->
 
-Type: Application
+Type: Application (non-`node_modules` code only)
 
 The [`punycode`][] module is deprecated. Please use a userland alternative
 instead.