#738 Cleanup and move some small steps in multilevel synthesis

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• Don't create a new list for the partial specifications, instead store them in the tree nodes.
• (user-visible) Give the partial specifications an hierarchical name to make the tree structure visible.
• (user-visible) The output directory is now always created.
• (user-visible) The partial specifications are always written (though before that depended on creating the directory, so arguably this is not a separate change).
• (user-visible) If the output directory exists, the partial specifications that already exist within it are no longer removed.
• Tree node can create a Box to describe itself.
• (user-visible) Tree node content is shown in terms of the included CIF plants and requirements rather than group index numbers at stdout.
• Updated test expectations:
  • Partial specs are renamed to their hierarchical name.
  • Expected output changed due to printing the included CIF plants and requirements.

Addresses #738