Configure ruff to ignore F821 in notebooks

Ruff does not understand Jupyter notebook cell execution order,
so it reports undefined name errors for variables that are defined
in earlier cells. This is a false positive for notebooks.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: justaddcoffee

pyproject.toml

@@ -88,5 +88,11 @@ extend-exclude = [
   "src/mcp_literature_eval/datamodel/mcp_literature_eval.py",
 ]
 
+# Ref.: https://docs.astral.sh/ruff/
+[tool.ruff]
+# Ignore F821 (undefined name) in notebooks - ruff doesn't understand Jupyter cell execution order
+[tool.ruff.lint.per-file-ignores]
+"notebook/*.ipynb" = ["F821"]
+
 [tool.uv.sources]
 metacoder = { git = "https://github.com/ai4curation/metacoder.git", branch = "codex-disable-shell-tool" }