重构程序文件目录结构并更新相关路径引用

- 创建新的目录结构：research/、tools/（含子目录）和apps/
- 移动核心理论文件到research/core-theory/
- 移动天山理论文件到research/specialized/
- 重组tools/目录为多个子目录：content-generation/、data-processing/等
- 更新所有文档中的路径引用，包括README.md、项目结构说明.md等
- 更新工作流文件和脚本中的路径引用
- 更新文档索引文件中的路径引用

.gitea/workflows/publish.yml

@@ -38,8 +38,8 @@ jobs:
       - name: 生成 EPUB/HTML 文档
         if: contains(github.event.head_commit.message, '[publish:ebook]') || contains(github.event.pull_request.title, '[publish:ebook]')
         run: |
-          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/generate_ebook.py --output_format epub
-          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/generate_ebook.py --output_format html
+          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/content-generation/generate_ebook.py --output_format epub
+          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/content-generation/generate_ebook.py --output_format html
 
       - name: 生成 Podcast 音频
         if: contains(github.event.head_commit.message, '[publish:podcast]') || contains(github.event.pull_request.title, '[publish:podcast]')
@@ -47,7 +47,7 @@ jobs:
           # 假设有一个 Markdown 文件作为 Podcast 脚本的来源
           # 例如：core-theory/cultural_logic_system.md
           mkdir -p artifacts/podcast
-          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/generate_podcast.py --text_file core-theory/cultural_logic_system.md --output_audio artifacts/podcast/cultural_logic_podcast.mp3
+          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/content-generation/generate_podcast.py --text_file core-theory/cultural_logic_system.md --output_audio artifacts/podcast/cultural_logic_podcast.mp3
 
       - name: 生成视频
         if: contains(github.event.head_commit.message, '[publish:video]') || contains(github.event.pull_request.title, '[publish:video]')
@@ -55,7 +55,7 @@ jobs:
           # 假设有一个 Markdown 文件作为视频脚本的来源
           # 例如：historical-research/geopolitical-codes/Y音正统性与地缘政治密码_完整理论框架.md
           mkdir -p artifacts/video
-          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/generate_video.py --text_file historical-research/geopolitical-codes/Y音正统性与地缘政治密码_完整理论框架.md --output_video artifacts/video/geopolitical_codes_video.mp4 --audio_path artifacts/podcast/cultural_logic_podcast.mp3
+          ./documentation/analysis/phallic-worship-analysis/venv/bin/python3 tools/content-generation/generate_video.py --text_file historical-research/geopolitical-codes/Y音正统性与地缘政治密码_完整理论框架.md --output_video artifacts/video/geopolitical_codes_video.mp4 --audio_path artifacts/podcast/cultural_logic_podcast.mp3
 
       - name: 上传生成物 (Artifacts)
         uses: actions/upload-artifact@v3