fixref

name	fixref
description	Use when you need to resolve placeholder citations (e.g., surname_year) or missing bibliography entries in the LaTeX thesis by querying NotebookLM context and InspireHEP.

Fix Reference (fixref) Workflow

Overview

A systematic workflow to resolve placeholder citations in LaTeX documents, retrieve the correct paper metadata using context-aware NotebookLM queries, fetch standard BibTeX via InspireHEP, and integrate them safely into the main bibliography without creating duplicates.

When to Use

• When encountering placeholder \cite{surname_year} keys in thesis chapters.
• When expanding or verifying the bibliography for specific sections.
• Callable explicitly via /fixref [section].

Discovery & Execution Pipeline

The workflow proceeds in 5 distinct phases:

Phase 1: Identification & Preparation

1. Call source_registry to ensure notebook sources are loaded if needed.
2. Read the target .tex document (e.g., chapter_02/sections/2.1...tex) and isolate all missing or placeholder citations. Look closely for patterns like \cite{Surname_Year}.
3. Check the central bibliography.bib file to see if those exact placeholder keys somehow already exist, or to map existing valid citations.

Phase 2: NotebookLM Contextual Resolution

For citations not found directly in the bib file:

1. Extract the paragraph of text surrounding the placeholder citation.
2. Query NotebookLM (id: 1b7df790-7858-4fc8-879c-39f41238c4ae) with the context paragraph and the placeholder name.
3. Prompt Structure: "Based on the thesis sources in this notebook, identify the correct paper for the placeholder citation Surname_Year. Here is the context: '[Context]'. Provide the full title, authors, and Notebook ID/bib-key if available."

Phase 3: Duplication Check

1. Take the full paper title returned by NotebookLM.
2. Run a Select-String or grep search on bibliography.bib using exact Title/Author keywords to ensure the paper isn't already present under a different bib-key (e.g., Smith:2020 vs Smith_2020).
3. If it exists, note the existing valid bib-key.

Phase 4: External BibTeX Fetching

For papers confirmed totally missing:

1. (Optional) If NotebookLM didn't provide standard identifiers (arXiv ID, DOI, Inspire ID), do a quick web search to find them using the title and authors.
2. Use the inspirehep MCP server (mcp_inspirehep_get_bibtex) with the identified arXiv ID or DOI to fetch the perfectly formatted inspirehep standard BibTeX.
3. Note the standard texkey provided by InspireHEP (e.g., Kafexhiu:2014cua).

Phase 5: Implementation & Verification

1. Append the newly retrieved BibTeX blocks to the bottom of bibliography.bib.
2. Clean up any obvious duplicate entries discovered during Phase 3.
3. Update the .tex file, systematically replacing the placeholder keys with the standard texkeys (both newly retrieved ones and pre-existing validated ones).
4. Run a final uniqueness check (e.g., PowerShell Select-String) on the .tex file's \cite{} commands to confirm every single key now exists in bibliography.bib.

Common Mistakes

• Skipping Title Search: Fetching BibTeX directly from InspireHEP and injecting it before checking bibliography.bib by title. This inherently creates silent duplicate entries with differing keys. Always do Phase 3.
• Wrong NotebookLM Context: Asking NotebookLM blindly for "Smith 2018" without providing the LaTeX paragraph. "Smith 2018" could be any of 50 papers; the context defines which mechanism/result is being cited.
• Orphan LaTeX Edits: Updating the bibliography.bib but forgetting to map the new key directly back into the .tex file.

Quick Reference Commands

List all citations in a tex file: Use the built-in grep_search tool with a regular expression on the target .tex file:

{
  "SearchPath": "/path/to/target/section.tex",
  "Query": "\\\\cite\\{([^}]+)\\}",
  "IsRegex": true
}

Find a paper by title in bibliography: Use the built-in grep_search tool on the central bibliography.bib file:

{
  "SearchPath": "/path/to/bibliography.bib",
  "Query": "Unique words from title",
  "IsRegex": false,
  "CaseInsensitive": true
}