feat: Complete project reorganization

- Reorganize core-theory into 6 thematic subdirectories (01-06)
- Clean up root directory, move files to appropriate locations
- Create comprehensive README files for navigation
- Add new academic papers and research content
- Implement English naming convention for better indexing
- Total: 42 core theory files organized, 7 READMEs created

Key improvements:
- Clear hierarchical structure (foundational → matrix → analysis → empires)
- Better discoverability with detailed navigation guides
- Scalable framework for future content expansion
- AI-friendly organization for indexing and processing

GEMINI.md

@@ -0,0 +1,49 @@
+# GEMINI.md - Project Overview
+
+## Directory Overview
+
+This directory contains the "胡汉三千年" (Hu-Han Three Thousand Years) project, a comprehensive knowledge base and research project. The project's goal is to re-examine Chinese history and its significance in world history from a new perspective.
+
+The content is primarily written in Markdown and organized into several categories:
+
+*   **`core-theory/`**: Contains the core theoretical framework of the research.
+*   **`historical-research/`**: Holds research papers on specific historical topics.
+*   **`academic-papers/`**: Contains academic papers on various subjects.
+*   **`literary-works/`**: Includes creative and analytical literary works.
+
+The project uses **Sphinx** to generate a documentation website from the Markdown files.
+
+## Key Files
+
+*   **`README.md`**: Provides a high-level overview of the project's vision, core insights, and structure.
+*   **`PROJECT_STRUCTURE.md`**: Details the layout and purpose of the directories within the project.
+*   **`FINAL_DISCOVERY_SUMMARY.md`** and **`PROJECT_BREAKTHROUGH.md`**: Summarize the key findings and breakthroughs of the research project.
+*   **`documentation/sphinx-docs/`**: Contains the configuration for the Sphinx documentation builder.
+    *   **`conf.py`**: The main Sphinx configuration file.
+    *   **`index.rst`**: The root document for the Sphinx site.
+*   **`build_docs.sh`**: A shell script that builds the Sphinx documentation into HTML.
+*   **`serve_docs.sh`**: A shell script that builds the documentation (if necessary) and serves it on a local web server.
+
+## Usage
+
+The primary way to interact with this project is by building and viewing the documentation website.
+
+### Building the Documentation
+
+To build the HTML documentation, run the following command in your terminal:
+
+```bash
+./build_docs.sh
+```
+
+This script will install the necessary Python dependencies (like Sphinx) and generate the website in the `documentation/sphinx-docs/_build/html` directory.
+
+### Viewing the Documentation
+
+To view the documentation locally, run the following command:
+
+```bash
+./serve_docs.sh
+```
+
+This will start a local web server. You can then open your web browser and navigate to **http://localhost:8000** to view the project's documentation website.