refactor: symmetric config layout and root CONTRIBUTING docs (#502)

* refactor: reorganize mdbook config and contributing docs

* fix: correct preprocessor relative paths in book.toml configs

The preprocessor command paths had one extra ../ level, resolving
outside the repo root. Fix from ../../../../tools/ to ../../../tools/.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

CONTRIBUTING/reference_guide.md

@@ -0,0 +1,38 @@
+# Reference Citation Guide / 参考文献引用方式
+
+All references are maintained in `mlsys.bib`.
+
+所有参考文献统一维护在 `mlsys.bib` 中。
+
+## Adding Bibliography Entries / 添加文献条目
+
+Add a BibTeX entry to `mlsys.bib`. Before adding, search for existing keys to avoid duplicates:
+
+在 `mlsys.bib` 中添加 BibTeX 格式的条目，添加前请先检索是否已存在同名 key：
+
+```bibtex
+@inproceedings{cnn2015,
+  title    = {CNN},
+  author   = {xxx},
+  year     = {2015},
+  keywords = {xxx}
+}
+```
+
+## In-text Citations / 正文引用
+
+A space is required before the citation directive:
+
+引用时前面需要有一个空格：
+
+1. Single reference / 单篇参考文献
+   ```
+   This article references the paper :cite:`cnn2015`
+   这篇文章参考了论文 :cite:`cnn2015`
+   ```
+
+2. Multiple references separated by commas / 多篇参考文献用逗号分隔
+   ```
+   This article references the papers :cite:`cnn2015,rnn2015`
+   这篇文章参考了论文 :cite:`cnn2015,rnn2015`
+   ```