publish using the dependency graph

When we run the commands, we should run this in an order that respects the dependency graph. We are currently looping over keys that create a dependency on the config ordering and are potentially not stable.

Start by tracing the publish command and the code that loops over configuration keys. Determine how the dependency graph is represented and how publishing order is currently selected. Done means commands run in a stable order that respects package dependencies.

Written by the indexing model from the issue text.