chapter-outline

name	chapter_outline
description	Research assistant that generates detailed, structural chapter outlines by synthesizing thesis context, local references, and NotebookLM insights.

Thesis Chapter Outlining Skill

This skill orchestrates the creation of deep, structurally robust chapter outlines for a PhD thesis. It calls the other thesis skills in sequence to build a comprehensive foundation, then synthesizes everything into a detailed outline.

Target Notebook

• Name: thesis references
• ID: 1b7df790-7858-4fc8-879c-39f41238c4ae

Prerequisites

• A target chapter directory (e.g., chapter_01).
• Access to outline.md (root thesis outline).

Workflow Steps

Step 0: Knowledge Retrieval

Before starting research, check for existing insights relevant to this chapter.

→ Call knowledge skill (retrieve mode) for the target chapter topic
→ Input: chapter title/topic from outline.md
→ Output: any pre-existing insights that can inform or skip research steps

If relevant knowledge files exist, use them to skip or accelerate subsequent research steps (e.g., if definitions are already extracted, skip that portion of literature research).

Step 1: Context Analysis

Understand where this chapter fits in the larger picture.

1. Read Root Outline: view_file outline.md. Identify the chapter's Scope, Key Contribution, Section Structure, and how it connects to the previous and next chapters.
2. Check Existing Artifacts: Look for any existing files in the chapter directory (references.md, chapter_outline.md, etc.) from prior work.

Step 2: Source Registry

Run the source_registry skill to obtain categorized source IDs.

→ Call source_registry skill
→ Obtain: author_paper_ids, review_ids, general_ids

This step is required before any NotebookLM queries.

Step 3: Literature Research

Run the literature_research skill to produce the chapter's references.md and data table.

→ Call literature_research skill for the target chapter
→ Input: chapter sections from outline.md, source IDs from Step 2
→ Output: chapter_XX/references.md (with data table + bib-key lookups)

Follow the granular per-subsection approach defined in the literature_research skill.

Step 4: Review Analysis

For the key review articles identified in Step 3, run review_analysis to extract detailed, citation-ready content.

→ Call review_analysis skill
→ Input: specific 002) source IDs for the most relevant reviews
→ Output: structured extraction notes, saved to .agent/knowledge/

Focus on reviews that will be heavily cited in this chapter.

Step 5: Paper Analysis (if applicable)

If an author paper is inserted in or near this chapter, run paper_analysis to extract key contributions and transition points.

→ Call paper_analysis skill
→ Input: specific 001) source ID(s) for papers relevant to this chapter
→ Output: methodology summary, key results, contribution statement, transition notes

Refer to the paper-to-chapter mapping in the paper_analysis skill.

Step 6: Structural Research

Use NotebookLM directly to study how experts structure arguments on this chapter's topic.

mcp_notebooklm_notebook_query(
    notebook_id="1b7df790-7858-4fc8-879c-39f41238c4ae",
    query="What is the detailed structure of [Reference X] regarding [Topic]? 
           List the section headers and summarize the argumentation flow. 
           How do they transition from [Concept A] to [Concept B]?",
    source_ids=<review_ids>
)

Focus on:

• How experts order their arguments
• How they introduce complex concepts
• How they transition between topics

Step 7: Draft chapter_outline.md

Create (or update) chapter_XX/chapter_outline.md.

Synthesis: Combine:

• Chapter requirements from outline.md
• References from references.md (Step 3)
• Review extractions (Step 4)
• Paper contributions and transitions (Step 5)
• Structural best practices (Step 6)

Format: Use a nested structure:

# Chapter [XX]: [Title]

## Connections
- **Previous Chapter**: [How this chapter follows from the previous one]
- **Next Chapter**: [How this chapter leads into the next one]
- **Inserted Paper**: [If applicable, which paper is inserted and its key contribution]

## [X.0] Chapter Introduction
**Goal**: Provide a brief, untitled opening (2–4 paragraphs) that orients the reader before the first numbered section. This text appears at the start of the chapter with no section heading.
**Narrative**: Follow a funnel structure:
- Opening context: broad motivation for the chapter's topic
- The central question this chapter addresses
- Chapter roadmap: one-sentence preview of each main section (X.1, X.2, …) and how they connect
- Bridge to the thesis: how the chapter's content feeds into the rest of the thesis

## [X.1] [Section Title]
**Goal**: [What this section achieves in the argument]
**Narrative**: [How the story progresses through this section]

### [X.1.1] [Subsection Title]
- Key point 1 → cite [Reference] (Sec X.X)
- Key point 2 → cite [Reference]
- **Figure**: [description] → from [arXiv:XXXX.XXXXX], Fig. N
- Transition: [How this leads to the next subsection]

### [X.1.2] [Subsection Title]
- ...

## [X.2] [Section Title]
...

## Chapter Summary
- [Key takeaway 1]
- [Key takeaway 2]
- [Bridge to next chapter / inserted paper]

Rules:

• Chapter Introduction (X.0): Mandatory for every chapter. Untitled in the final output — provides opening paragraphs before the first numbered section
• H2 sections: Main structural divisions
• H3 subsections: Specific logical steps
• Bullets: Key points with specific reference citations
• Figure annotations: Mark key literature figures with **Figure**: [description] → from [arXiv:ID], Fig. N. These signal to section_drafting Step 4b which figures to fetch and download
• Transitions: Explicitly note how each section leads to the next
• Connections: First section documents how this chapter connects to the rest of the thesis

Step 8: Review and Refine

Iterate on the draft:

1. Logical Flow: Does Section A naturally lead to Section B? Are prerequisites defined before use?
2. Coverage: Are all topics from outline.md addressed?
3. Weakness Check: Are there "jumps" in logic? Missing definitions?
4. Self-Contained vs. Connected: The chapter should stand on its own while explicitly linking to previous/future chapters.
5. Insert Transitions: If a paper is inserted after this chapter, does the outline build up to it properly?

Output

• chapter_XX/chapter_outline.md — the detailed structural outline
• chapter_XX/references.md — references with data table (produced in Step 3)
• .agent/knowledge/ — key insights saved via the knowledge skill (produced in Steps 3–5)