without the datastore_path parameter i was getting un-predictable results for retaining data, so i have made the habit of using it. just what i do...
keep in mind that not every type of query needs an index, if the updated time on the file is incrementing then the dev_appserver probably is finding that you do not need to add an index. see more http://code.google.com/appengine/docs/python/config/indexconfig.html you are correct that when running the app under dev_appserver.py that index.yaml should be updated by the app engine SDK
