app.yaml の handlers 定義の順序に気をつけましょう、というオチ。悲しい。
以下、引用：
9. The order that handlers in app.yaml, web.xml, and appengine-web.xml are specified in matters
One of the more common and subtle mistakes people make when configuring their app is to forget that handlers in the application configuration files are processed in order, from top to bottom. For example, when installing remote_api, many people do the following:
handlers:
- url: /.*
script: request.py
- url: /remote_api
script: $PYTHON_LIB/google/appengine/ext/remote_api/handler.py
login: admin
The above looks fine at first glance, but because handlers are processed in order, the handler for request.py is encountered first, and all requests - even those for remote_api - get handled by request.py. Since request.py doesn't know about remote_api, it returns a 404 Not Found error. The solution is simple: Make sure that the catchall handler comes after all other handlers.
The same is true for the Java runtime, with the additional constraint that all the static file handlers in appengine-web.xml are processed before any of the dynamic handlers in web.xml.
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