pub deps --json will work slightly different with the Pub Workspaces feature, so we need to change how we parse the JSON slightly (see dart-lang/pub#4330).

Currently we use kind field on a package to know if it is a direct/dev/transitive dependency, but that data will no longer be accurate because the solve is for all packages in the Pub Workspace and not the one where we executed pub get. Instead, we should look at the dependencies list for the package (and a new dev_dependencies that may be added as the solution to dart-lang/pub#4330).

For an initial fix, we could continue to execute pub deps in each package and just ensure we filter the results correctly - but as a further optimisation we should run only in workspace roots or non-workspace packages, and produce multiple package nodes at the root of the tree from a single pub deps --json result.