integrate

/integrate — Thesis Integration Skill

Purpose

After completing a reading session, this skill weaves key arguments, quotes, and concepts from reading notes into the thesis manuscript. It ensures new material is placed in the right chapter and section, with proper attribution and minimal disruption to existing structure.

Trigger Words

This skill activates on: integrate, weave in, add to thesis, /integrate.

Workflow

1. Scan the specified notes file(s) for the ## Thesis Connections table and ## Key Arguments section. If the user does not specify which notes file, ask. If the user says "all pending", scan all notes files with Status: completed (not yet integrated). When guards/ is present, first run npm --prefix guards run lint:notes -- {files}: report any file that fails the contract lint and exclude it from the plan explicitly — never silently skip a non-conforming file. A source whose notes carry Evidence status: abstract_only or metadata_only must not be woven in as supporting evidence; flag it instead.

2. Read target chapter files in chapters/ to identify insertion points. Use Grep to find relevant sections, existing citations of the same author, and thematic paragraphs where the new material fits.

3. Present an integration plan as a table. Do not execute any changes yet.

   ## Integration Plan: {Author} -- {Title}
   
   | # | Source Concept | Chapter | Section | Insertion Type | Preview |
   |---|---------------|---------|---------|----------------|---------|
   | 1 | {concept} | Ch{N} | {section ref} | new paragraph / expand existing / add citation / add footnote | {first 10 words of proposed text} |
   
   Estimated word count delta: +{N} words across {N} chapters.
   Proceed? (yes / edit plan / cancel)
   

4. Wait for user approval. The user may:

   • Say "yes" or "proceed" to execute the plan as shown.
   • Say "edit plan" and specify changes (remove a row, change a section, etc.).
   • Say "cancel" to abort.