Scholar Deep Research

End-to-end academic research workflow that turns a question into a cited, structured report. Built for depth: multi-source federation, transparent ranking, citation chasing, and a mandatory self-critique pass before the report ships.

When to use

Explicit triggers: "literature review", "research report", "state of the art", "survey the field", "what's known about X", "deep research on Y", "systematic review", "scoping review", "compare papers on Z".

Proactive triggers (use without being asked):

• User asks a factual question whose honest answer is "it depends on the literature"
• User frames a research plan and needs the background section
• User is drafting a paper intro/related-work and hasn't yet scoped prior work
• User proposes a method and asks whether it's novel

Do not use when: a single known paper answers the question, the user wants a tutorial (not a survey), or they're debugging code.

Guiding principles

1. Scripts over vibes. Every search, dedupe, rank, and export step runs through a script in scripts/. The same input should produce the same output. Do not improvise ranking or counting by eye.
2. Sources are federated, not singular. OpenAlex is the primary backbone (free, 240M+ works, no key). arXiv, Crossref, and PubMed fill gaps. MCP tools (Semantic Scholar / Brave) are enrichment, not dependency — if they time out, research continues.
3. State is persistent. Everything goes through research_state.json. Queries ran, papers seen, decisions made, phase progress. Research becomes resumable and auditable.
4. Citations are anchors, not decorations. Every non-trivial claim in the draft carries [^id] where id matches a paper in state. Unanchored claims are treated as hallucinations and fail the gate.
5. Saturation, not exhaustion, is the stop signal. A phase ends when a new round of search adds <20% novel papers AND no new paper has >100 citations.
6. Self-critique is a phase, not a checkbox. Phase 6 reads the draft with adversarial intent. Its output goes into the report appendix.

The 8-phase workflow (Phase 0..7)

Phase 0: Scope       → decompose question, pick archetype, init state
Phase 1: Discovery   → multi-source search, dedupe
Phase 2: Triage      → rank, select top-N for deep read
Phase 3: Deep read   → extract evidence per paper
Phase 4: Chasing     → citation graph (forward + backward)
Phase 5: Synthesis   → cluster by theme, map tensions
Phase 6: Self-critique → adversarial review, gap finding
Phase 7: Report      → render archetype template, export bibliography

Each phase writes to research_state.json before advancing. If the user pauses or a session crashes, the next run reads the state and picks up from the last completed phase.

Phase 0 — Scope

Step 0 — Check for skill updates (silent, once per day). Before anything else, run:

python scripts/check_update.py