The first step in working with ExtJS 6 is to generate a new workspace (at least in my case).
sencha generate workspace test-workspace
We see something interesting right away. A new workspace.json file is created in your workspace. Just as app.json has become the central configuration point for ExtJS applications, workspace.json is the new central configuration point for workspaces.
The new workspace.json contains configuration for build.dir, packages.dir and packages.extract. Packages.extract is an entirely new configuration that identifies a new folder in which automatically downloaded packages are installed. By default, this is packages/remote. In addition, when local packages are generated, they are generated in the packages/local folder. For backwards compatibility, packages installed in the base packages folder are still used.
The old workspace/sencha.cfg is still available (and contains the old configs that are now overridden by workspace.json). This file also includes workspace.theme.dir which I assume can also be overridden in workspace.json. I've never configured themes at the workspace level before, so I'm not entirely sure what the expected behavior is here.