Improve and extend documentation and changes in README.md

[thesteganos]

This commit addresses several documentation shortcomings:

• Corrected a broken link in the main README's Table of Contents.

• Added a link to the existing MCP setup guide (docs/mcp_setup.md) in the main README.

• Created a new comprehensive guide docs/knowledge_and_rag.md detailing the knowledge base features and RAG capabilities. This file is linked in the main README.

• Created a new guide docs/hacking_and_customization.md that covers advanced topics such as prompt engineering for personas and the dynamic behavior system. This file is linked in the main README.

• Updated docs/architecture.md to include cross-references to the new, more detailed knowledge_and_rag.md and hacking_and_customization.md pages, improving discoverability of information.

• Corrected outdated information:

  • Removed "MCP" and "Knowledge and RAG Tools" from the "Coming soon" section as these features are already implemented/merged.
  • Refined the "Hacking Edition" section to remove the note about it being merged into the main branch in a future release, as this has occurred.

• Improved navigation and information discovery:

  • Updated several links to point to more specific sections within the documentation (e.g., Installation, Usage guides).
  • Added new links from the main README to relevant documentation pages for features like MCP