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Makefile.in: enable 3-stage bootstrap using packages
The bootstrap stage 1 registry and the main registry are moved to the workspace directory. So this is a new requirement, that the bootstrap must be done inside a workspace. We can easily check for and create a workspace.json file in the parent directory if necessary. dylan-tool is built from source first, then the registry is updated using dylan-tool update, then the bootstrap is much the same as always.
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