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].