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

documentation/planning/FINAL_PROJECT_STRUCTURE.txt

@@ -0,0 +1,83 @@
+.
+├── academic-papers
+│   ├── cultural-studies
+│   ├── methodology
+│   ├── papers
+│   └── symbol-belief
+├── archive
+│   └── temp-files
+├── CLAUDE.md
+├── config
+├── core-theory
+│   ├── 01-foundational-concepts
+│   ├── 02-matrix-theory
+│   ├── 03-character-analysis
+│   ├── 04-accounting-operation
+│   ├── 05-three-empires-framework
+│   ├── 06-legacy-docs
+│   └── README.md
+├── documentation
+│   ├── analysis
+│   ├── docs
+│   ├── document_index.json
+│   ├── document_index_report.json
+│   ├── documents
+│   ├── overview
+│   ├── planning
+│   ├── project-overview
+│   ├── rfcs
+│   └── sphinx-docs
+├── GEMINI.md
+├── historical-research
+│   ├── architecture
+│   ├── cultural-transmission
+│   ├── geography
+│   ├── geopolitical-codes
+│   ├── geopolitical-continuity
+│   ├── han-global-revolution
+│   ├── imperial-seal
+│   ├── islamic-china
+│   ├── jade-road
+│   ├── religious-transmission
+│   ├── turkic-studies
+│   └── yanda-origins
+├── images
+│   ├── 0_序
+│   ├── 0 序：令人又敬又畏的_忽里勒台_大会
+│   ├── 1.1 第一帝国：长城（上）
+│   ├── 1.2 第一帝国：长城（下）
+│   ├── 2.1 第二帝国：运河（上）
+│   ├── 2.2 第二帝国：运河（下）
+│   ├── 3.1 第三帝国：圐圙（1）
+│   ├── 3.2 第三帝国：圐圙（2）
+│   ├── 3.3 第三帝国：圐圙（3）
+│   └── 3.4 第三帝国：圐圙（4）
+├── literary-works
+│   ├── analysis
+│   ├── poetry
+│   └── profiles
+├── output
+│   └── ascii_cultural_viz
+├── README.md
+├── scripts
+│   ├── apply_simplified_config.sh
+│   ├── build_docs.sh
+│   ├── rename_documents.sh
+│   ├── serve_docs.sh
+│   ├── start_local_docs_server.sh
+│   └── test_plugins.sh
+└── tools
+    ├── ai-tools
+    ├── analysis
+    ├── diagrams
+    ├── document-management
+    ├── generate_ebook.py
+    ├── generate_podcast.py
+    ├── generate_video.py
+    ├── image-processing
+    ├── setup
+    ├── test_milvus_gpu.py
+    ├── text-processing
+    └── visualization
+
+65 directories, 16 files