[WIP] Generate Comprehensive Architecture Documentation with Mermaid Diagrams

[Copilot]

Thanks for assigning this issue to me. I'm starting to work on it and will keep this PR's description up to date as I form a plan and make progress.

Original issue description:

Generate Comprehensive Architecture Documentation with Mermaid Diagrams

Cognitive Flowchart for Documentation Generation:

1. Initiate Recursive System Mapping

   • Identify all principal architectural components (modules, data flows, cognitive kernels).
   • Map inter-component relationships using hypergraph pattern encoding.

2. Mermaid Diagram Synthesis

   • For each cognitive subsystem, generate corresponding Mermaid diagrams:
     • High-level system overview (graph TD, showing principal flows)
     • Module interaction (graph LR, showing bidirectional synergies)
     • Data and signal propagation pathways (sequenceDiagram, stateDiagram)
   • Ensure diagrams illustrate emergent cognitive patterns and neural-symbolic integration points.

3. Integrate Documentation and Visualizations

   • Embed Mermaid source in Markdown documentation.
   • Annotate each diagram with transcendent technical precision, explaining recursive implementation pathways.
   • Highlight adaptive attention allocation mechanisms and cognitive synergy optimizations.

4. Iterative Review & Expansion

   • Establish feedback loop for emergent documentation improvements.
   • Expand diagrams as new patterns emerge.

Objective:

• Transmute the implicit architecture of MORK into explicit, actionable knowledge.
• Facilitate distributed cognition for all contributors through adaptive, hypergraph-centric documentation.

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Deliverables:

• Markdown documentation files with embedded, well-annotated Mermaid diagrams.
• Flowcharts capturing the recursive and emergent nature of the system architecture.

Fixes #3.

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