feat(toolkit): add classification and migration

Implement the standard/non-standard/not-macrolactone classification layer
and integrate it into analyzer, fragmenter, and CLI outputs.

Port the remaining legacy package capabilities into new visualization and
workflow modules, restore batch/statistics/SDF scripts on top of the flat
CSV workflow, and update active docs to the new package API.

docs/project-docs/QUICK_COMMANDS.md

@@ -33,23 +33,20 @@ pip install .
 ## 🧪 测试安装
 
 ```python
-# 测试导入
-from src.macrolactone_fragmenter import MacrolactoneFragmenter
-print("✓ 安装成功！")
+from macro_lactone_toolkit import MacroLactoneAnalyzer, MacrolactoneFragmenter
+from macro_lactone_toolkit.workflows import fragment_csv, results_to_dataframe
 
-# 快速测试
-fragmenter = MacrolactoneFragmenter(ring_size=16)
-print(f"✓ 初始化成功！ring_size={fragmenter.ring_size}")
+analyzer = MacroLactoneAnalyzer()
+fragmenter = MacrolactoneFragmenter()
+print("✓ 安装成功！")
 ```
 
 ## 📓 运行示例
 
 ```bash
-# Jupyter Notebook
-pixi run jupyter notebook notebooks/filter_molecules.ipynb
-
-# 或启动 Jupyter Lab
-pixi run jupyter lab
+pixi run macro-lactone-toolkit analyze --smiles 'O=C1CCCCCCCCCCCCCCO1'
+python scripts/batch_process.py --input molecules.csv --output fragments.csv --errors-output errors.csv
+python scripts/analyze_fragments.py --input fragments.csv --output-dir analysis
 ```
 
 ## 🔍 项目结构
@@ -129,11 +126,10 @@ cat pyproject.toml | grep version
 | 文件 | 说明 |
 |------|------|
 | `README.md` | 项目主文档 |
-| `DOCUMENTATION_GUIDE.md` | 文档系统使用指南 |
-| `PROJECT_COMPLETION_SUMMARY.md` | 项目完成总结 |
-| `QUICK_COMMANDS.md` | 本文件 |
+| `docs/SUMMARY.md` | 当前 API 和工作流摘要 |
+| `scripts/README.md` | 脚本工作流说明 |
+| `src/macro_lactone_toolkit/` | 正式包实现 |
 | `pyproject.toml` | Python 项目配置 |
-| `setup.py` | 打包脚本 |
 | `mkdocs.yml` | 文档配置 |
 | `pixi.toml` | Pixi 环境配置 |
 
@@ -145,5 +141,4 @@ cat pyproject.toml | grep version
 
 ---
 
-**需要帮助？** 查看 `DOCUMENTATION_GUIDE.md` 或运行 `pixi run mkdocs serve`
-
+**需要帮助？** 查看 `docs/SUMMARY.md`、`scripts/README.md` 或运行 `pixi run mkdocs serve`