Is it possible to do custom builds on the GCE instance thats building and deploying your code? I.e. run scripts to minify JS, etc? Or is this something you would do locally and make sure the artifacts were checked into git?
Similarly if you run full functional tests (selenium in a browser), can these be started on the gce instance and be part of the "test" step?
We discourage checking in artifacts (e.g., minified JS) into source control because it defeats the purpose in a lot of ways.
Currently there is no support for custom build/test steps but the builds that are done for Java apps are done using Jenkins so you can imagine that in the fullness of time anything Jenkins supports would also be supported as a pre-deploy step. I don't have any specific details though, as my work has been focused on the GitHub integration.
Absolutely, this is a big thing we're working on, giving visibility into failures. Having the push go to GitHub means our options for error reporting are a little more limited, unfortunately.
One thing you may want to check is that your app.yaml is in the root directory of the master branch. That's where we look currently to figure out what to deploy.
If you'd like me to investigate further you can email jasonhall@google.com and I'll look into what's going on.