[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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[Copilot]

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[drzo]

implement

[Copilot]

implement

Implementation complete! I've created comprehensive architecture documentation with Mermaid diagrams covering the entire P-Lingua framework. The documentation includes:

📐 System Architecture - High-level design patterns, data flows, and component relationships
🔧 Component Deep Dive - Internal architecture of parser, simulator, and code generator
💡 Usage Examples - Practical demonstrations with working P-Lingua code
📚 Navigation Index - Complete documentation structure with performance analysis

All diagrams use Mermaid syntax for maintainability and clearly illustrate the recursive and emergent nature of the membrane computing architecture. The documentation transmutes the implicit MORK architecture into explicit, actionable knowledge as requested.

Commit: 9240cd6

[drzo]

joyful