Milestone Five - #11
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This PR focuses on making Cypher understandable, reviewable, and easier to evaluate from the repository itself. It adds a user guide, examples guide, expanded technical code tour, and OpenMC comparison note, while updating existing documentation to reflect the current container-first workflow and the near-term status of planned pip/possible Conda installation paths. The new docs explain the discovery, authoring, XML export, schema-header, execution, and Cymetric handoff workflows without requiring readers to reconstruct project intent from chat history or source code.
This PR also adds notebook-style examples for the bakery, once-through, and EG transition scenarios, alongside script versions for the larger examples. Bakery remains the small runnable smoke-test example, while the once-through and EG transition notebooks demonstrate how larger fuel-cycle scenarios can be built up in Cypher section by section. The advanced scenarios are clearly marked as software authoring examples rather than validated or citable fuel-cycle models, and the documentation records the current limitation around complex nested stream serialization as follow-on work.