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.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.