Hello Azrayl,
I understand that you would like to block your web application from being indexed by Google and you are using a subdomain of a custom domain.
I was able to find some information indicating several techniques here[
1][
2] but please note that blocking indexing is not related to Google App Engine, rather Search Engine Optimization. Google App Engine is just where applications live.
From the first link we see advice that you may add a noindex meta tag to the page’s HTML code.
You may additionally return a noindex header in the HTTP request. They go on to say that when the Googlebot sees the tag or header, it will ignore that page and not place it in Google Search results.
I’ve found webmaster
forums that you may use for further questions. I invite you to tell them what you’ve tried to stop indexing your application. Maybe you were initially on the proper track. As this Google Group is meant for App Engine, perhaps those forums would be better suited.
I hope this helps.