Bibliography

Procedure:

1. Identify the citation system — Read the first 3-5 inline citations. Classify as author-year (APA/Harvard), numbered (Vancouver), or other. See CITATION_FORMATS.md.

2. Extract all inline citations — Scan the entire body text (everything above the References/Bibliography section). For author-year systems, capture both parenthetical (Smith, 2024) and narrative Smith (2024) forms. For numbered systems, capture all [N] references. Normalize each to a lookup key.

3. Extract all bibliography entries — Parse the References section. Extract author surname(s), year, and title from each entry. Generate matching lookup keys.

4. Cross-reference: citations → bibliography — For each inline citation, find the matching bibliography entry. Record any citations that have no match ("cited but not listed").

5. Cross-reference: bibliography → citations — For each bibliography entry, find at least one matching inline citation. Record any entries with no match ("listed but not cited").

6. Scan for informal mentions — Build a surname list from the bibliography. Scan body text for these surnames appearing outside of formal citations. Flag instances like "Tufte argued that..." where a formal citation is missing.

7. Generate the audit report — Use the template in AUDIT_REPORT_TEMPLATE.md. Include counts, status assessment, and specific issues with locations.

The bidirectional check:

  BODY TEXT                          BIBLIOGRAPHY
  ─────────                          ────────────
  (Smith, 2024)  ──────────────────► Smith, J. (2024)...     ✓
  (Jones, 2023)  ──────────────────► Jones, K. (2023)...     ✓
  Lee (2024)     ───── ? ──────────►                         ✗ CITED BUT NOT LISTED
                                     Adams, R. (2022)...     ✗ LISTED BUT NOT CITED
  "Tufte argued" ─── informal ─────►                         ⚠ INFORMAL MENTION

2. Fix Mode

Resolve issues found during audit. Always run audit first.

Invoke with: /bibliography fix manuscript.md

Procedure:

1. Run audit (if not already done) to identify all issues.

2. Cited but not listed — For each missing entry:

   • Search for the full reference details in the manuscript context (footnotes, supplementary material, or related files)
   • If details are available, add a properly formatted entry to the bibliography
   • If details are unknown, add a placeholder: [TODO: Complete reference for Smith (2024)]
   • Place the entry in correct order (alphabetical for author-year, sequential for numbered)

3. Listed but not cited — For each orphaned entry:

   • Read the entry's title and topic
   • Scan the manuscript for passages where this reference is relevant
   • If a relevant passage exists, add an inline citation at the appropriate location
   • If no relevant passage exists, flag the entry for potential removal but do NOT remove automatically — the author may intend to cite it in a future revision

4. Informal mentions — For each informal mention:

   • Identify the referenced work (match to bibliography or determine the needed reference)
   • Convert to a formal citation: "Tufte argued..." → "Tufte (2001) argued..."
   • If the work is not in the bibliography, add it (see step 2)

5. Re-run audit to verify all issues are resolved. Report the before/after comparison.

3. Format Mode

Validate and standardize reference formatting to a target style.

Invoke with: /bibliography format --style apa manuscript.md

Procedure:

1. Identify the target style — Use the --style flag (apa, vancouver, chicago) or detect from the manuscript. See REFERENCE_STYLES.md.

2. Check each bibliography entry against the target style rules:

   • Author name format (initials vs. full names, punctuation)
   • Year placement
   • Title capitalization (sentence case vs. title case)
   • Journal name formatting (italics, abbreviation)
   • Volume/issue/page format
   • DOI format
   • Punctuation and ordering

3. Check inline citations for style consistency:

   • Correct use of & vs. and
   • Correct et al. threshold
   • Correct punctuation within parenthetical citations

4. Report issues with specific entries and the required corrections.

5. Apply corrections if requested, preserving the semantic content while fixing formatting.

Boundary with Other Skills

Common Problems

Handling Edge Cases

Multiple Works by Same Author in Same Year

• APA: (Smith, 2024a) and (Smith, 2024b) — add letter suffixes
• Vancouver: separate numbers, no special handling needed
• Chicago: (Smith 2024a) and (Smith 2024b)

Secondary Citations (Citing Through Another Work)

• APA: (Smith, 2020, as cited in Jones, 2024) — only Jones appears in bibliography
• Flag if Smith also appears in bibliography (redundant)

Works with No Author

• APA: Use title in citation: ("Article Title," 2024)
• Vancouver: Organization name or title
• Match carefully — these are easy to miss in cross-referencing

Manuscripts with .bib Files

• Check the .bib file for all entries
• Also check the rendered bibliography (some .bib entries may not be \cited)
• Keys like \cite{smith2024} map to @article{smith2024,...} in the .bib file

Quality Checks

Before finalizing any bibliography work:

• Every inline citation matches exactly one bibliography entry
• Every bibliography entry is cited at least once
• No informal author mentions without formal citations
• Entries follow a single, consistent style
• Entry ordering matches the style (alphabetical or by appearance)
• Author names are spelled consistently between inline citations and bibliography
• Years match between inline citations and bibliography entries
• For numbered systems: numbers are sequential with no gaps or duplicates
• For author-year systems: entries with same author/year have letter suffixes (a, b, c)
• DOIs are included where available

Related Files

• CITATION_FORMATS.md — Detection patterns for citation and bibliography formats
• REFERENCE_STYLES.md — APA, Vancouver, Chicago formatting rules
• AUDIT_REPORT_TEMPLATE.md — Structured output template for audit results