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This commit introduces a complete, specialized framework for Axiom Prompt Engineering tailored to the Food Science and Bakery R&D domain.

The system is structured into four key components:
- Foundational knowledge base (`research/bakery_science_fundamentals.md`)
- Core scientific principles as axioms (`protocols/bakery_axioms.md`)
- A suite of multi-modal prompt templates (`templates/bakery_rd/`) for various tasks like recipe generation, troubleshooting, and research analysis. Each template supports 'Accurate', 'Efficient', and 'Creative' optimization modes.
- Practical examples (`examples/bakery_rd/`) demonstrating the usage of the templates.

This personalized system provides a robust and flexible tool for bakery R&D professionals to leverage LLMs effectively.
This commit introduces a complete, specialized framework for Axiom Prompt Engineering tailored to the Food Science and Bakery R&D domain.

The system is structured into four key components:
- Foundational knowledge base (`research/bakery_science_fundamentals.md`)
- Core scientific principles as axioms (`protocols/bakery_axioms.md`)
- A suite of multi-modal prompt templates (`templates/bakery_rd/`) for various tasks like recipe generation, troubleshooting, and research analysis. Each template supports 'Accurate', 'Efficient', and 'Creative' optimization modes.
- Practical examples (`examples/bakery_rd/`) demonstrating the usage of the templates.

This personalized system provides a robust and flexible tool for bakery R&D professionals to leverage LLMs effectively.
This commit extends the Bakery R&D system with two new, highly practical prompt templates:

1.  **Ingredient Specification Sheet Generator:** An interactive template that analyzes user input for completeness. If critical data is missing, it intelligently asks clarifying questions before generating the technical document. This is ideal for handling new or poorly documented ingredients.

2.  **Shelf-Life Study Designer:** A template that generates a comprehensive, science-based protocol for shelf-life studies, including sampling plans, analytical parameters, and acceptance criteria.

The documentation has been updated to include these new tools, and a new example is provided to illustrate the interactive functionality.
This commit further enhances the Bakery R&D system with two new templates for core professional workflows:

1.  **Ingredient Application Testing Protocol:** Generates a structured protocol for testing new ingredients, including a detailed step-by-step checklist for bench work and a professional report outline.

2.  **Commercial Formula Optimizer:** A template designed to create and optimize commercially viable recipes. It forces the language model to consider and balance sensory quality with critical business factors like cost-in-use, production line compatibility, and batch-to-batch stability.

The documentation has been updated to reflect these additions.
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