Thank you for the information shared so far. I am still a little unclear 
about what you are attempting though. 

>From the information provided, I understand you are attempting to connect 
to your App Engine Standard Application(that is, the application code has 
already been deployed). While SSHing to the Instance of an App Engine 
flexible application is possible[1], for App Engine standard, this is not 
available at the moment. So, I am unclear how you mean trying to connect to 
specific directory within the App Engine standard server. I am unclear also 
about what you mean running App Engine in Ubuntu Server. 

If what you are trying to achieve is to have some form of source code 
management and version control, perhaps your team should consider using 
Cloud Source Repositories[2]. Directories in Source repositories could 
browsed in Cloud Shell[3]. 

[1]https://cloud.google.com/sdk/gcloud/reference/app/instances/ssh
[2]https://cloud.google.com/appengine/docs/flexible/python/debugging-an-instance#connecting_to_the_instance
[3]https://cloud.google.com/source-repositories/docs/browsing-files-in-cloud-shell#open-a-repository-in-cloud-shell

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