writing-lit-review

Literature Review & Source Materialization

Gather, discover, and materialize all sources into references/ so downstream phases (setup, draft, cite-check) operate on local files only.

Prerequisites: Brainstorm complete. User has confirmed topic, angle, and audience. Research themes identified (3-6 themes from brainstorm).

brainstorm (themes + angle)
     ↓
 LIT REVIEW (this skill)
     ├─ Channel 1: Scholar + Consensus → Paperpile → rclone → references/*.pdf
     ├─ Channel 2: Readwise (personal reading) → export → references/*.md
     ├─ Channel 3: NLM deep research → Obsidian web clipper (user-driven)
     ↓
 setup (PRECIS + OUTLINE + sources.bib)

## The Iron Law of Source Materialization

NO SETUP WITHOUT MATERIALIZED SOURCES. This is not negotiable.

Before PRECIS.md or OUTLINE.md exist, references/ must contain local copies of every source you plan to cite. A PRECIS built on metadata-only sources leads to claims that cite-check cannot verify.

If you catch yourself writing sources.bib entries without local files backing them, STOP.

Three Channels — No Overlap

Each channel owns a distinct source type. Never route a source through the wrong channel.

Channel	Owns	Discovery tool	Storage	Materialization
Paperpile	Academic papers (journals, working papers, SSRN)	Scholar + Consensus	Paperpile library	rclone copy PDF → references/<bibkey>.pdf
Readwise	User's personal reading (articles, reports, PDFs they've highlighted)	Readwise search	Readwise Reader	readwise reader-get-document-details → references/<bibkey>.md
Obsidian	Web sources from deep research (SEC speeches, blog posts, comment letters, news)	NLM deep research	Obsidian vault via web clipper	User clips URL → link/copy to references/

Channel routing decision

Is it an academic paper (journal article, working paper, SSRN)?
  YES → Paperpile channel
  NO  → Has the user already read/highlighted it?
          YES → Readwise channel
          NO  → Found via NLM deep research?
                  YES → Obsidian channel (user clips the URL)
                  NO  → Flag as gap

Channel Facts

• Draft agents cite only what exists in references/ — sources deferred to "later" never enter the draft. On unmaterialized PRECIS runs, cite-check has flagged ~30% of citations as NOT_IN_STORE, forcing the user to backtrack and gather sources mid-draft. Deferring materialization to "show progress faster" is anti-helpful on its own terms.
• Readwise stores web captures, not canonical PDFs. An academic paper routed through Readwise lacks the authoritative text and metadata cite-check needs — send academic papers through Paperpile.
• Scholar returns metadata only; Paperpile stores the PDF. A Scholar hit without a Paperpile add (then rclone) leaves nothing to materialize.
• Cite-check verifies claims against local text in references/ — every source you cite, including web sources like SEC speeches, needs a local copy (Obsidian clip or Readwise export). A bib entry without a backing file is an unverifiable citation.

Process

Step 1: Set Up References Directory

mkdir -p references

Step 2: Academic Sources — Paperpile Channel

For each research theme from brainstorm, dispatch parallel search agents:

Agent(
  subagent_type="workflows:librarian",
  prompt="Search Google Scholar and Consensus for academic papers about [THEME].
  For each paper found, return: title, author(s), year, journal, DOI if available.
  Focus on empirical papers and seminal works. Return top 5 most relevant."
)

Launch all theme agents in a single message (parallel execution).

After results return:

1. Deduplicate across themes
2. Check Paperpile for each paper: paperpile search "<title>" --json
3. Add missing papers to Paperpile:
   • If DOI available: paperpile add <doi>
   • If no DOI: paperpile find-and-add "<citation>" (when available)
   • Manual: user adds via Paperpile UI
4. Batch copy PDFs from Paperpile to references/:

cd ${CLAUDE_SKILL_DIR}/../cite-check
bun materialize-sources.ts \
  --bib ~/Google\ Drive/My\ Drive/resources/Paperpile/paperpile.bib \
  --refs <project>/references \
  --debug

This runs rclone copy --files-from for all Paperpile PDFs in one call.

Step 3: Personal Reading — Readwise Channel

Search Readwise for sources the user has already been reading about the topic:

Agent(
  subagent_type="workflows:librarian",
  prompt="Search Readwise Reader for documents related to [TOPIC].
  Search by these queries: [theme1], [theme2], [theme3].
  For each document found, return: title, author, document_id, category.
  Only return documents the user has actually saved (not search results from elsewhere)."
)

After results return, materialize-sources.ts handles Readwise export automatically — entries without file fields in the bib are searched in Readwise by title and exported as markdown.

Step 4: Web Sources — NLM Deep Research Channel

For web sources not in Paperpile or Readwise, use NLM to discover them:

1. Create NLM notebook for the project (if not already created):

   nlm create "<project title>"
   

   Add key source PDFs and URLs to the notebook.

2. Discover related sources via NLM:

   nlm discover-sources <notebook-id> "<research theme>"
   nlm research <notebook-id> "<broader research question>"
   

3. Save discovered URLs to Readwise Reader for scraping and export: Write discovered URLs to a file (one per line, format: URL | Title | Author), then:

   cd ${CLAUDE_SKILL_DIR}/../cite-check
   bun materialize-sources.ts \
     --save-urls <url-file> \
     --refs <project>/references \
     --tag <project-tag> \
     --debug
   

   This saves each URL to Readwise Reader (which scrapes and converts to markdown), then exports the content to references/.

4. Fallback: Obsidian web clipper (manual, for sites Readwise can't scrape):

   These web sources need manual clipping via Obsidian web clipper:
   - [Title 1]: [URL 1]
   

   The Writing vault IS the project directory, so clipped files land directly in references/.

Step 5: Build/Update sources.bib

After materialization, ensure references/sources.bib has entries for every source in references/:

1. For Paperpile PDFs: extract bib entries from paperpile.bib for cited keys
2. For Readwise exports: create @misc or @article bib entries from the markdown frontmatter
3. Set file fields to point to local copies: file = {<bibkey>.pdf} or file = {<bibkey>.md}

Step 6: Gap Analysis

Run the materializer in audit mode to check coverage:

cd ${CLAUDE_SKILL_DIR}/../cite-check
bun materialize-sources.ts \
  --bib <project>/references/sources.bib \
  --refs <project>/references \
  --drafts <project>/drafts \
  --debug

Present gaps to user:

=== Source Materialization Summary ===
Paperpile PDFs: X copied
Readwise articles: Y exported
Gaps (need manual action): Z
  - [bibkey1]: "Title" → needs Obsidian web clip
  - [bibkey2]: "Title" → not found anywhere

Red Flags

• About to write sources.bib entries without local files in references/ → STOP. Bib entries without files are unverifiable; materialize first, then build the bib.
• About to route an academic paper through Readwise → STOP. Readwise has web captures, not canonical PDFs with proper metadata — use Paperpile.
• About to add by DOI without searching Paperpile first → STOP. The paper may already be in Paperpile; search first, add only if missing.
• About to move to setup without running gap analysis → STOP. Gaps found during drafting are 10x harder to fill.
• About to create sources.bib manually instead of from the Paperpile export → STOP. Manual entries get typos, missing fields, and wrong citekeys — extract from paperpile.bib.

Gate: Exit Lit Review

Before proceeding to writing-setup:

1. IDENTIFY: references/ directory exists with source files

2. RUN: ls references/*.pdf references/*.md | wc -l — count local source files

3. READ: Check materialize-sources.ts gap analysis output

4. VERIFY: All three conditions met:

   • (a) At least 80% of brainstorm sources have local copies in references/
   • (b) Any gaps are explicitly flagged and acknowledged by user
   • (c) references/sources.bib exists with file fields pointing to local copies

5. CLAIM: Only if steps 1-4 pass, write the gate artifact, THEN proceed to writing-setup. writing-setup's PreToolUse hook blocks until this file exists — the artifact is what proves materialization actually happened:

   mkdir -p .planning && cat > .planning/LIT_REVIEW_COMPLETE.md <<EOF
   ---
   status: APPROVED
   gate: lit-review
   gap_rate: ${GAP_RATE:-unknown}
   ---
   Lit review gate passed: sources materialized to references/, sources.bib has file fields, gap rate within 20% (or gaps acknowledged by user).
   EOF
   

A gap rate above 20% is a BLOCKER. Ask the user: "20% of sources are missing. Should we search more, or proceed with known gaps?"

Do not write status: APPROVED until sources are genuinely materialized. The artifact certifies local copies in references/ — forging it sends setup into a PRECIS built on sources that cite-check cannot verify.

No Pause Between Steps

After completing each step, IMMEDIATELY start the next. Do NOT:

• Ask "should I continue to Readwise search?"
• Summarize what you just found
• Wait for confirmation between channels

The three channels are independent — run them all, then present the combined results.

Phase Complete → Proceed to Setup

After lit review gate passes, immediately proceed to writing-setup:

Read ${CLAUDE_SKILL_DIR}/../writing-setup/SKILL.md and follow its instructions.