Example: Joint Mainline Logic and Experiment Review

User request: First check whether the thesis mainline closes from the introduction through the conclusion, then determine whether the experiment chapters read more like a project report than a thesis discussion.

Recommended module order:

1. logic
2. experiment

Commands:

uv run python $SKILL_DIR/scripts/analyze_logic.py main.tex
uv run python $SKILL_DIR/scripts/analyze_experiment.py main.tex

Note: full-document mode in analyze_logic.py includes the introduction funnel, chapter mainline, and C3 introduction-conclusion closure by default. Add --section 绪论 to focus on one chapter (both Chinese chapter names and English keys are accepted).

Expected output:

• First identify any misalignment among the introduction, contribution origins, and conclusion.
• Then identify missing comparison, mechanism explanation, limitation discussion, and future work in experiment chapters.
• Report the two issue classes through their respective modules instead of merging them into generic “expression optimization.”