Fix slow tests sometimes failing

In some situations we reloaded the workspace in the tests after having reported
to be ready. There's two fixes here:
1. Add a version to the VFS config and include that version in progress reports,
so that we don't think we're done prematurely;
2. Delay status transitions until after changes are applied. Otherwise the last
change during loading can potentially trigger a workspace reload, if it contains
interesting changes.

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