Organize documentation files and clean repository root

AGENTS.md

@@ -1,7 +1,8 @@
 # Agent Guidelines
 
-This repository uses Codex agents to automate certain development tasks. Contributors should review the task list in [CODEX.md](CODEX.md) before starting work. The roadmap in [docs/ROADMAP.md](docs/ROADMAP.md) explains the intended project phases.
+This repository uses Codex and Jules agents to automate certain development tasks. Contributors should review the task list in [CODEX.md](CODEX.md) before starting work. The roadmap in [docs/ROADMAP.md](docs/ROADMAP.md) explains the intended project phases.
 
 - Follow the tasks in CODEX.md when adding new files or features.
 - Keep docs/ROADMAP.md updated as milestones are reached.
+- Remember that you are not alone, we are a team of humans and AI working together.
 

README.md

@@ -8,16 +8,16 @@ Knowledge3D (K3D) is an initiative from EchoSystems AI Studios to build an open
 
 ## White‑paper overview
 
-The white‑paper "A 3D Vector Universe Standard for High‑Dimensional AI Knowledge" describes the core objective: create a universal 3D data format that lets users fly through interconnected datasets as if visiting planets in space.  Success is defined by knowledge navigability—intuitive traversal and reduced cognitive load—and by technical metrics such as frame rate, query latency and adoption by researchers.
+The white-paper ["A 3D Vector Universe Standard for High-Dimensional AI Knowledge"](docs/papers/3d_vector_universe_standard.docx) describes the core objective: create a universal 3D data format that lets users fly through interconnected datasets as if visiting planets in space.  Success is defined by knowledge navigability—intuitive traversal and reduced cognitive load—and by technical metrics such as frame rate, query latency and adoption by researchers.
 
 Other companion documents expand on this vision:
 
-* **AI model integration.** "AI Models and 3D Knowledge (K3D) Databases" explores how neural models could inhabit the same 3D data world, enabling immersive visualization and shared interaction.
-* **Augmented reality use cases.** "Integrating Augmented Reality and AI: New Frontiers in Training, Learning, and Exploration" outlines how AR headsets can overlay K3D scenes onto the real world for education and field work.
-* **CAD/vector database fusion.** "Merging CAD and Vector Database Concepts into a 3D Knowledge Visualization Standard" and "Using AutoCAD’s 3D Vector Format as an AI Vector Database" discuss storing vector embeddings inside CAD-like geometry files so that standard 3D tools become knowledge browsers.
-* **Science fiction influence.** "From Sci-Fi to Reality: How Tron's Grid, The Matrix, Star Wars, Star Trek, and *The Jetsons* Foreshadowed Our Future" highlights pop-culture milestones that predicted immersive 3D data interfaces.
+* **AI model integration.** ["AI Models and 3D Knowledge (K3D) Databases"](docs/papers/ai_models_k3d_databases.docx) explores how neural models could inhabit the same 3D data world, enabling immersive visualization and shared interaction.
+* **Augmented reality use cases.** ["Integrating Augmented Reality and AI: New Frontiers in Training, Learning, and Exploration"](docs/papers/ar_ai_frontiers.docx) outlines how AR headsets can overlay K3D scenes onto the real world for education and field work.
+* **CAD/vector database fusion.** ["Merging CAD and Vector Database Concepts into a 3D Knowledge Visualization Standard"](docs/papers/merging_cad_vector_db.docx) and ["Using AutoCAD’s 3D Vector Format as an AI Vector Database"](docs/papers/autocad_3d_vector_format.docx) discuss storing vector embeddings inside CAD-like geometry files so that standard 3D tools become knowledge browsers.
+* **Science fiction influence.** ["From Sci-Fi to Reality"](docs/papers/sci_fi_to_reality.docx) highlights pop-culture milestones that predicted immersive 3D data interfaces.
 * **Historical inspiration.** [Lessons from Early 3D Interfaces and Apollo 11](docs/fsn_apollo_inspiration.md) reflects on SGI's 3D file navigator \(as seen in *Jurassic Park*\) and NASA's modular software practices.
-* **Collaborative research.** "Spatial Web K3D Gemini Deep Research Report 2" combines insights from **OpenAI GPT o3 Deep Research** with a final write‑up produced by **Google Gemini 2.5 Pro/Flash**.
+* **Collaborative research.** ["Spatial Web K3D Gemini Deep Research Report 2"](docs/reports/spatial_web_k3d_gemini_report.docx) combines insights from **OpenAI GPT o3 Deep Research** with a final write‑up produced by **Google Gemini 2.5 Pro/Flash**.
 * **Temporal agents and knowledge graphs.** [Temporal Agents with Knowledge Graphs](docs/openai_temporal_agents_cookbook.md) distills takeaways from the [OpenAI cookbook notebook](https://github.com/openai/openai-cookbook/blob/main/examples/partners/temporal_agents_with_knowledge_graphs/temporal_agents_with_knowledge_graphs.ipynb).
 * **Eval-driven pipeline design.** [Eval-Driven System Design](docs/openai_eval_driven_system_design_cookbook.md) shows how rigorous evaluations steer autonomous K3D workflows.
 * **Voice agents via MCP.** [MCP-Powered Agentic Voice Framework](docs/openai_mcp_voice_agents_cookbook.md) demonstrates orchestrating tool-calling voice interfaces with the Model Context Protocol.
@@ -26,18 +26,18 @@ Other companion documents expand on this vision:
 * **3D embedding plots.** [Visualizing Embeddings in 3D](docs/openai_visualizing_embeddings_3d_cookbook.md) applies PCA to project high-dimensional vectors into spatial plots.
 * **Vector store integrations.** [Vector Database Guides](docs/openai_vector_database_guides.md) catalog storage options for semantic search.
 * **Dynamic tool execution.** [Dynamic Code Interpreter for Agents](docs/openai_dynamic_code_interpreter_cookbook.md) explores on-the-fly code generation and execution with o3-mini.
-* **Manus AI perspective.** The PDFs "The K3D Advantage: A Paradigm Shift for Internal AI Memory" and "The K3D Catalyst: Fostering Human-Like Reasoning and Intuition in AI" are both signed by **Manus AI**.
+* **Manus AI perspective.** The PDFs ["The K3D Advantage: A Paradigm Shift for Internal AI Memory"](docs/reports/manus_k3d_advantage.pdf) and ["The K3D Catalyst: Fostering Human-Like Reasoning and Intuition in AI"](docs/reports/manus_k3d_catalyst.pdf) are both signed by **Manus AI**.
 * **AR vision with an AI coauthor.** "Integrating Augmented Reality and AI: New Frontiers in Training, Learning, and Exploration" expands on Daniel Campos Ramos' ideas in partnership with an **AI assistant**.
-* **Interactive demo.** The HTML file "K3D Gemini report" showcases a simple web report generated using **Google Gemini**.
-* **ChatGPT agent research.** "ChatGPT Agent - K3D paradigm research" collects exploratory notes from early conversations with the OpenAI model.
-* **Industry impact deck.** "ChatGPT Agent - Impact of the K3D Paradigm on BIM and Additive Manufacturing" and the spreadsheet "ChatGPT Agent - Impact_Domains.xlsx" map potential use cases across sectors.
-* **Claude's perspective.** "Claude - Collective Intelligence in Shared K3D Space" summarizes Anthropic's take on collaborative 3D knowledge worlds.
-* **Concept slides.** "From_Pages_to_Spaces.pptx" visualizes how web pages could evolve into immersive spaces.
-* **Deep research notes.** "Gemini DeepResearch Report" chronicles brainstorming sessions prior to the Gemini coauthored paper.
-* **Perplexity AI review.** "Expert Assessment - Perplexity AI" offers an outside evaluation of the K3D paradigm from **Perplexity AI**.
-* **Portuguese reflections.** "Como eu, como IA, me beneficiaria ao integrar uma" and "Is this idea too different that it requires a comp" capture additional ChatGPT analysis in Portuguese.
-* **Audio discussion.** "Spatial Web & K3D_ Your Future of Immersive Knowledge and AI Collaboration.mpga" captures an informal conversation about the Spatial Web.
-* **Screenshot preview.** "Screenshot_20250730_153941.png" shows an early build of the planned 3D viewer.
+* **Interactive demo.** The HTML file ["K3D Gemini report"](docs/reports/k3d_gemini_report.html) showcases a simple web report generated using **Google Gemini**.
+* **ChatGPT agent research.** ["ChatGPT Agent - K3D paradigm research"](docs/reports/chatgpt_k3d_research.docx) collects exploratory notes from early conversations with the OpenAI model.
+* **Industry impact deck.** ["ChatGPT Agent - Impact of the K3D Paradigm on BIM and Additive Manufacturing"](docs/presentations/chatgpt_k3d_bim_am.pptx) and the spreadsheet ["ChatGPT Agent - Impact_Domains.xlsx"](docs/reports/chatgpt_impact_domains.xlsx) map potential use cases across sectors.
+* **Claude's perspective.** ["Claude - Collective Intelligence in Shared K3D Space"](docs/papers/claude_collective_intelligence.pdf) summarizes Anthropic's take on collaborative 3D knowledge worlds.
+* **Concept slides.** ["From_Pages_to_Spaces.pptx"](docs/presentations/from_pages_to_spaces.pptx) visualizes how web pages could evolve into immersive spaces.
+* **Deep research notes.** ["Gemini DeepResearch Report"](docs/reports/gemini_deep_research_report.docx) chronicles brainstorming sessions prior to the Gemini coauthored paper.
+* **Perplexity AI review.** ["Expert Assessment - Perplexity AI"](docs/reports/perplexity_ai_assessment.docx) offers an outside evaluation of the K3D paradigm from **Perplexity AI**.
+* **Portuguese reflections.** ["Como eu, como IA, me beneficiaria ao integrar uma"](docs/papers/portuguese_ai_integration.docx) and ["Is this idea too different that it requires a comp"](docs/papers/portuguese_is_idea_too_different.docx) capture additional ChatGPT analysis in Portuguese.
+* **Audio discussion.** ["Spatial Web & K3D: Your Future of Immersive Knowledge and AI Collaboration.mpga"](docs/spatial_web_k3d_discussion.mpga) captures an informal conversation about the Spatial Web.
+* **Screenshot preview.** ["Screenshot_20250730_153941.png"](docs/viewer_preview.png) shows an early build of the planned 3D viewer.
 
 ## EchoSystems Action Plan
 
@@ -51,7 +51,7 @@ See [`echo_systems_k_3_d_action_plan_v_0.md`](docs/reports/echo_systems_k_3_d_ac
 
 ## TeleKnowledge vision
 
-The companion paper *"Towards an Interactive __TeleKnowledge__ Internet: A 3D Virtual World for Businesses, Humans, and AI"* expands on the long‑term ambition for Knowledge3D.  It imagines a **Spatial Web** where self‑hosted virtual buildings replace today’s static pages.  Using open protocols such as the IEEE 2874 Hyperspace Transaction Protocol (HSTP) and its HSML modeling language, any organization could serve a richly interactive 3D environment under its own domain while still linking seamlessly to others.  Built‑in decentralized identifiers control access so both humans and AI agents can explore knowledge spaces safely and transparently.
+The companion paper *["Towards an Interactive __TeleKnowledge__ Internet: A 3D Virtual World for Businesses, Humans, and AI"](docs/papers/teleknoledge_internet.docx)* expands on the long‑term ambition for Knowledge3D.  It imagines a **Spatial Web** where self‑hosted virtual buildings replace today’s static pages.  Using open protocols such as the IEEE 2874 Hyperspace Transaction Protocol (HSTP) and its HSML modeling language, any organization could serve a richly interactive 3D environment under its own domain while still linking seamlessly to others.  Built‑in decentralized identifiers control access so both humans and AI agents can explore knowledge spaces safely and transparently.
 
 ## Potential collaborators
 
@@ -100,7 +100,7 @@ npm run dev
 
 This launches a local server that renders `examples/sample_output.gltf` and shows point IDs on hover.
 
-![Viewer preview](Screenshot_20250730_153941.png)
+![Viewer preview](docs/viewer_preview.png)
 
 ## Licensing