.meteor/packages in new apps now contains "standard-app-packages", which implies
the standard set of packages like mongo-livedata. There is no special-casing in
initFromAppDir. This line has been added to all the examples, etc.
There's a new concept of "upgraders". "meteor run-upgrader app-packages" will
add standard-app-packages to the app, as well as all of the package in the app's
packages/ directory (an unrelated change since 0.6.4). This will be integrated
soon with "meteor update"; run-upgrader is essentially for testing.
project.add_package no longer adds packages that are already there.