Source Verify

Source Verification

Verify that citations in a manuscript are real, accurate, and that quoted text actually appears in the source. Operates as a domain-specific audit-fix-loop: extract citations, run checks, score, fix, re-check. (See the audit-fix-loop skill for the canonical doctrine — auditor≠fixer, substrate-gate, anti-grind; this skill's substrate is citation/quote resolution.)

Announce: "Using source-verify to check citations against Paperpile and source documents."

What This Skill Checks

┌──────────────────────────────────────────────────────────┐
│  CHECK 1: EXISTENCE (mechanical)                          │
│  Does this cited work exist in paperpile.bib?            │
│  → grep paperpile.bib for author + title + year          │
│  → If not found: flag as UNVERIFIED (may still exist)    │
└──────────────────────────────────────────────────────────┘
                        │
                  Exists in bib?
                        ▼
┌──────────────────────────────────────────────────────────┐
│  CHECK 2: ACCURACY (mechanical)                           │
│  Are the citation fields correct?                        │
│  → Compare volume, issue, pages, year against bibtex     │
│  → Flag any mismatches as FIELD_ERROR                    │
└──────────────────────────────────────────────────────────┘
                        │
                  Fields correct?
                        ▼
┌──────────────────────────────────────────────────────────┐
│  CHECK 3: QUOTE VERIFICATION (outsourced to RAG)          │
│  Does the quoted text appear in the source?              │
│  → readwise chat: "Verify this exact quote from [Author] │
│  → rga against downloaded PDF (fallback)                 │
│  → NLM generate-chat against notebook (fallback)         │
│  → Flag QUOTE_NOT_FOUND or QUOTE_MISMATCH               │
└──────────────────────────────────────────────────────────┘
                        │
                  Quotes verified?
                        ▼
┌──────────────────────────────────────────────────────────┐
│  CHECK 4: CLAIM GROUNDING (outsourced to RAG)             │
│  Does the cited source actually support the claim?       │
│  → readwise chat or NLM generate-chat                    │
│  → These systems answer ONLY from source text            │
│  → Flag UNSUPPORTED or CONTRADICTED                      │
└──────────────────────────────────────────────────────────┘

Checks 1-2 run on every invocation (fast, mechanical). Check 3 runs when the footnote contains a direct quote. Check 4 runs only when the user explicitly requests claim grounding.

Independence Architecture

The key insight: verification must use external ground truth, never the agent's own memory. Two systems provide this:

┌─────────────────────────────────────────────────────────┐
│  VERIFIER HIERARCHY — QUOTES (try in order)              │
│                                                          │
│  1. Readwise highlights — User highlighted the passage.  │
│     readwise-custom highlights --search "quote fragment"  │
│     If found: verified against actual source text.       │
│     Fastest — no download, no LLM.                       │
│                                                          │
│  2. rga (local)    — Download PDF from Drive, search.    │
│     Deterministic text search inside PDFs.               │
│     No pdftotext needed — rga extracts text internally.  │
│                                                          │
│  3. NLM chat       — Add paper to a verification         │
│     notebook, then query.                                │
│     "Find this passage in [source]: '…'"                │
│     Grounded in NLM's ingested sources.                  │
│     Best for: OCR issues, paraphrased quotes.            │
│                                                          │
│  NEVER: Agent's own memory/training data.                │
│  That is the hallucination source, not a verifier.       │
└─────────────────────────────────────────────────────────┘

┌─────────────────────────────────────────────────────────┐
│  VERIFIER — CLAIM GROUNDING                              │
│                                                          │
│  NLM chat only — requires semantic understanding.        │
│  Readwise highlights are too fragmentary for claims.     │
│  rga is too literal for "does source support claim?"     │
└─────────────────────────────────────────────────────────┘

Why Readwise first for quotes: The user highlights important passages while reading. If a quote in the manuscript matches a Readwise highlight, it was captured directly from the source — strongest possible verification, zero cost.

Why NLM for claims: Claim grounding requires understanding what the source argues, not just matching strings. NLM chat answers from ingested full text with semantic comprehension.

Scope

Federal Case Verification via WRDS

The FJC Integrated Database (fjc_litigation.civil) contains all federal civil cases with plaintiff/defendant names, docket numbers, filing dates, districts, and nature-of-suit codes. Use it to verify that cited cases actually exist:

# Connect via SSH tunnel to WRDS
ssh wrds "echo \"SELECT plaintiff, defendant, docket, district, filedate
FROM fjc_litigation.civil
WHERE plaintiff ILIKE '%smith%' AND defendant ILIKE '%jones%'
AND filedate BETWEEN '2018-01-01' AND '2020-12-31'
LIMIT 10;\" | psql -h wrds-pgdata.wharton.upenn.edu -p 9737 -d wrds"

Matching strategy for case cites:

• Extract plaintiff and defendant names from the citation (e.g., "Smith v. Jones")
• Search fjc_litigation.civil with ILIKE on both fields
• Confirm year matches filedate
• For securities cases, filter nos = 850 (nature of suit: securities/commodities)

Audit Analytics (audit_corp_legal.f14_lit_legal_case) provides corporate legal cases with settlement amounts, exposure dates, and docket numbers — useful for verifying securities litigation specifically.

Limitations:

• casename field is sparsely populated — match on plaintiff/defendant instead
• State court cases are NOT covered (federal only)
• Appellate case names may differ from trial court names
• Very recent cases may have a lag before appearing in the database

Statutes are not yet verifiable — no structured database wired up. Flag as SKIPPED_NO_GROUND_TRUTH.

NEVER skip Checks 1-2 to jump straight to LLM-based verification.

Mechanical checks against paperpile.bib are deterministic and free. They catch the most common hallucinations (invented papers, wrong volume/pages) without any LLM judgment. Running LLM checks without running mechanical checks first is wasting expensive calls on problems a grep would catch.

Skipping the paperpile.bib check is NOT HELPFUL — the user publishes with unverified citations that may be hallucinated.

Step 0: Prerequisites

Download paperpile.bib

The bibtex file lives on Google Drive and must be downloaded fresh each run:

# Download paperpile.bib from Drive
gws drive files get --account eddyhu@gmail.com \
  --params '{"fileId": "1yxibJLr1-kF_gcf3UA6QlU5ulXgR50kX", "alt": "media"}' \
  -o /tmp/paperpile.bib

Always download fresh — the user may have added new papers since the last run.

Extract Footnotes

If the manuscript is DOCX, extract footnotes to structured text first. Use the bluebook-audit extraction infrastructure or python-docx:

# Quick extraction via python-docx
uv run --with python-docx python3 -c "
import docx, json, sys
doc = docx.Document(sys.argv[1])
fns = []
for i, fn in enumerate(doc.part.element.findall('.//{http://schemas.openxmlformats.org/wordprocessingml/2006/main}footnote')):
    fn_id = fn.get('{http://schemas.openxmlformats.org/wordprocessingml/2006/main}id')
    if fn_id and int(fn_id) > 0:
        text = ' '.join(p.text or '' for p in fn.iter('{http://schemas.openxmlformats.org/wordprocessingml/2006/main}t'))
        fns.append({'id': int(fn_id), 'text': text.strip()})
json.dump(fns, sys.stdout, indent=2)
" manuscript.docx > /tmp/footnotes.json

For plain text or markdown manuscripts, extract lines that look like footnotes (numbered references at the bottom or inline citations).

Step 1: Check 1 — Citation Existence

For each footnote, extract the cited author(s) and title, then search paperpile.bib:

# Search by author surname
rg -i "author.*Egan" /tmp/paperpile.bib

# Search by title fragment
rg -i "conflicting interests" /tmp/paperpile.bib

# Search by bibtex key pattern
rg "Egan2022" /tmp/paperpile.bib

Matching Strategy

Footnotes use Bluebook-abbreviated journal names; bibtex uses different abbreviations. Match on author surname + year first, then confirm with title keywords.

Classification

Step 2: Check 2 — Field Accuracy

For each VERIFIED citation, compare footnote fields against bibtex:

Journal abbreviation mismatches are tricky — Bluebook and bibtex use different abbreviation conventions. Flag only when the journal name is clearly wrong (e.g., completely different journal), not when it's a different valid abbreviation of the same journal.

Step 3: Check 3 — Quote Verification

For footnotes that contain direct quotes (text in quotation marks attributed to a source):

Tier A: Readwise Highlights (fastest — no download needed)

If the user highlighted the quoted passage in Readwise, it's already verified against the actual source text:

# Search for the quote text in highlights
readwise-custom highlights --search "quoted text fragment" --limit 10

# Or vector search with author filter
readwise readwise-search-highlights --vector-search-term "quoted text fragment" \
  --full-text-queries '[{"field_name": "document_author", "search_term": "Egan"}]'

A matching highlight confirms the quote exists in the source — Readwise captured it directly from the original document. Check that the highlight comes from the correct source (match author/title).

Tier B: rga (deterministic — download and search)

If the quote isn't in Readwise highlights, download the PDF from Drive and search:

# Find the PDF using the bibtex `file` field
# e.g., file = {All Papers/E/Egan et al. 2022 - Conflicting Interests...pdf}
gws drive files list --account eddyhu@gmail.com \
  --params '{"q": "name contains \"Egan et al. 2022 - Conflicting\" and mimeType = \"application/pdf\"", "fields": "files(id,name)", "pageSize": 1}'

# Download by file ID
gws drive files get --account eddyhu@gmail.com \
  --params '{"fileId": "<ID>", "alt": "media"}' -o /tmp/source.pdf

# Search for the quote (rga extracts PDF text internally — no pdftotext needed)
rga "the exact quoted text" /tmp/source.pdf

If rga finds it, the quote is QUOTE_VERIFIED — deterministic, no LLM needed.

Tier C: NLM Chat (semantic fallback)

If rga doesn't find an exact match (OCR issues, scanned PDF, or the quote is slightly paraphrased), add the paper to a verification NLM notebook and ask:

# Create a verification notebook (once per project)
nlm create "Source Verification"

# Add the paper
nlm add <notebook-id> /tmp/source.pdf

# Ask NLM to find the quote
nlm generate-chat <notebook-id> "Find this exact passage in the source: '[quoted text]'. Does it appear verbatim? If the wording differs, show the actual text from the source."

NLM chat is grounded in the ingested PDF — it can handle OCR artifacts and minor wording differences that trip up exact string matching.

Quote Match Classification

Step 4: Check 4 — Claim Grounding (Optional)

Only run when user explicitly requests deep verification. This checks whether the cited source actually supports the claim being made in the text (not just that the citation exists).

NLM Chat (grounded in source text)

Claim grounding requires semantic understanding — NLM chat is the right tool because it answers only from ingested sources.

nlm generate-chat <notebook-id> "The manuscript claims: '[claim from text]' and cites [Author (Year)]. Does the source support this claim? Answer: SUPPORTED, PARTIALLY_SUPPORTED, UNSUPPORTED, or CONTRADICTED. Provide the relevant passage from the source."

Requires: An NLM notebook with the cited sources loaded. If not already set up:

1. Create a verification notebook: nlm create "Source Verification — [Project]"
2. Add papers: download from Drive, then nlm add <notebook-id> /tmp/source.pdf
3. Or bulk import: nlm research "[topic]" --notebook <notebook-id> --source drive

Cross-source claims: When a claim synthesizes multiple papers, add all cited sources to the same notebook. NLM can then cross-reference them in a single query. For synthesized claims that draw on web-accessible sources (news, reports, public data), the deep-research skill is available as a supplementary check -- use it after NLM grounding to verify claims against broader web evidence. NLM remains the primary tool for source-specific grounding.

Classification

Scoring

Score = verified items / total checkable items, scaled to 0-10.

checkable = total_footnotes - SKIPPED_NO_GROUND_TRUTH
verified = VERIFIED + QUOTE_VERIFIED + CLAIM_SUPPORTED
score = (verified / checkable) * 10

Items with any finding (FIELD_ERROR, QUOTE_NOT_FOUND, UNVERIFIED, etc.) count against the score. QUOTE_UNCHECKED (source PDF unavailable) counts as checkable but not verified — it's an unresolved question, not a pass.

Default threshold: 9.5/10 (95% of checkable citations verified).

Audit-Fix Loop Integration

This skill is a domain-specific scorer for the audit-fix pattern. Its substrate is deterministic and binary — every citation either resolves against the bib or it doesn't; every quote either verifies against its source or it doesn't. So gate on the substrate directly, not a 0-10 composite (which here is just a noisy restatement of the same counts). The evaluator reads the finding counts from the transcript and refires until they hit zero.

/goal Source-verify [manuscript] is complete when .planning/SCORES.md shows ALL citations
resolved against paperpile.bib, ALL quotes verified via Readwise/rga/NLM, and ZERO UNVERIFIED
or QUOTE_NOT_FOUND findings remaining. (The 0-10 score is advisory — the zero-count substrate is
the gate.) Stop after 5 turns.

Iteration Protocol

Each turn under the active goal:

1. Audit: Run Checks 1-3 on all footnotes (Check 4 only if requested)
2. Score: Compute score, record in SCORES.md (the evaluator reads this)
3. Decide: Score >= 9.5? → end the turn; the /goal evaluator will mark the condition met. Score < 9.5? → fix and end the turn so the next iteration fires.
4. Fix: For each finding:
   • FIELD_ERROR → correct the volume/pages/year in the manuscript
   • QUOTE_MISMATCH → fix the quote to match the source text
   • QUOTE_NOT_FOUND → flag for user review (may need to remove quote or find correct source)
   • UNVERIFIED → search harder (try more bibtex key variants, try Drive search), or flag for user
   • CLAIM_UNSUPPORTED → flag for user review (rewrite claim or find better source)

State Files

VERIFY_AUDIT.md — current verification findings:

# Source Verification — Iteration N

## Summary
- Total footnotes: 85
- Checkable: 72 (13 case cites skipped)
- Verified: 68
- Findings: 4
- Score: 9.4/10

## Findings
| FN# | Check | Classification | Severity | Details |
|-----|-------|---------------|----------|---------|
| 12 | Existence | UNVERIFIED | CRITICAL | "Smith (2019)" not found in paperpile.bib |
| 34 | Fields | FIELD_ERROR | HIGH | Vol. 42 in footnote, vol. 44 in bibtex |
| 51 | Quote | QUOTE_MISMATCH | MEDIUM | "effect on returns" vs source: "impact on returns" |
| 67 | Quote | QUOTE_NOT_FOUND | CRITICAL | Quoted text not in cited PDF |

SCORES.md — score history (append-only):

| Iteration | Score | Findings | Key Issues |
|-----------|-------|----------|-----------|
| 1 | 8.2 | 6 | 2 UNVERIFIED, 2 FIELD_ERROR, 2 QUOTE issues |
| 2 | 9.1 | 3 | 1 UNVERIFIED (confirmed real), 2 QUOTE issues |
| 3 | 9.6 | 1 | 1 QUOTE_MISMATCH (minor) |

NEVER verify citations from your own memory or training data. Always use an external ground truth.

Citation hallucination happens because the LLM confabulates plausible-sounding references. The same LLM will confabulate plausible-sounding verification. Every check must go through an external system:

• Checks 1-2: paperpile.bib (mechanical grep — deterministic)
• Checks 3-4: Readwise chat, rga, or NLM chat (grounded in actual source text)
• NEVER: "I recall this paper exists" or "That quote sounds right"

Skipping external source checks is NOT HELPFUL — unverified citations damage the user's credibility when readers check them.

Verification Facts

• Hallucinated citations are designed to look plausible — "looks right" is the signature of a confabulated cite, not evidence of a real one. A citation is VERIFIED only when the matching bibtex entry is in hand; marking it VERIFIED from memory is an unverified claim presented as fact, and the agent's memory is the hallucination source, not a verifier.
• Hallucinated citations cluster in the middle and end of a manuscript, where writing fatigue hits — sampling the first footnotes misses the worst errors. Check ALL footnotes; the un-sampled footnote citing a non-existent paper is the one that causes the retraction.
• If rga can't find a quote, the quote may be fabricated or paraphrased — escalate to NLM chat as semantic fallback, and if still not found, flag QUOTE_NOT_FOUND. "Close enough" is not a match: either it matches or it's a QUOTE_MISMATCH, and presenting a near-quote as verified misrepresents the source — dishonest.
• A close-but-wrong volume number (42 vs 44) is a wrong citation; a reader following it lands on the wrong article. Fix to match the bibtex entry.
• Federal case cites CAN be checked (WRDS fjc_litigation.civil); state cases are SKIPPED_NO_GROUND_TRUTH — skip them explicitly, never silently.
• Self-verification is rubber-stamping: the checks run through a fresh audit agent and external ground truth, never the agent's own judgment of its own work.