feat(numbering): publish canonical numbering API

Add a public numbering module and route fragmenting, validation,
and scaffold preparation through the canonical numbering entry.

Rewrite the repository entry docs around the fixed numbering
contract, add MkDocs landing pages, and document the mirror
mapping used for medicinal-chemistry comparisons.

Also refresh the validation analysis reports to explain the
canonical-versus-mirrored numbering relationship.

mkdocs.yml

@@ -130,49 +130,25 @@ nav:
   - 首页:
     - index.md
     - 快速开始: getting-started.md
-    - 安装指南: installation.md
 
   - 用户指南:
     - user-guide/index.md
-    - MacrolactoneFragmenter 使用: user-guide/fragmenter-usage.md
     - 环编号系统: user-guide/ring-numbering.md
-    - 可视化功能: user-guide/visualization.md
-    - 批量处理: user-guide/batch-processing.md
-    - 数据导出: user-guide/data-export.md
-
-  - 教程与示例:
-    - tutorials/index.md
-    - 基础教程: tutorials/basic-tutorial.md
-    - 环数识别教程: tutorials/using-macro-lactone-analyzer.md
-    - 高级用法: tutorials/advanced-usage.md
-    - 使用案例: tutorials/use-cases.md
-
-  - API 参考:
-    - api/index.md
-    - MacroLactoneAnalyzer: api/macro-lactone-analyzer.md
-    - MacrolactoneFragmenter: api/macrolactone-fragmenter.md
-    - Fragment 数据类: api/fragment-dataclass.md
-    - 环编号模块: api/ring-numbering.md
-    - 可视化模块: api/ring-visualization.md
-    - 工具函数: api/utilities.md
 
   - 开发者指南:
     - development/index.md
-    - 贡献指南: development/contributing.md
     - 项目结构: development/project-structure.md
-    - 测试: development/testing.md
 
   - 项目文档:
     - project-docs/AGENTS.md
-    - 实现总结: project-docs/IMPLEMENTATION_SUMMARY.md
-    - 清理总结: project-docs/CLEANUP_SUMMARY.md
-    - 文档指南: project-docs/DOCUMENTATION_GUIDE.md
-    - 快速命令: project-docs/QUICK_COMMANDS.md
 
-  - 关于:
-    - about/index.md
-    - 更新日志: about/changelog.md
-    - 许可证: about/license.md
+not_in_nav: |
+  /SUMMARY.md
+  /plans/
+  /project-docs/CLEANUP_SUMMARY.md
+  /project-docs/DOCUMENTATION_GUIDE.md
+  /project-docs/IMPLEMENTATION_SUMMARY.md
+  /project-docs/QUICK_COMMANDS.md
 
 # Extra
 extra:
@@ -201,4 +177,3 @@ extra:
           note: >- 
             Thanks for your feedback! Help us improve this page by
             creating an issue.
-