Deep research

Deep Research

Classic deep research = search wide (100s) → screen → read deep (10s–20s) → synthesize.

Standalone — no pipeline prerequisite. Follow references/screening-funnel.md for target numbers.

Tool names are indicative — use the equivalents available in your environment (e.g. interactive question widgets, sub-agent/task launchers, web search/fetch tools).

When to use (vs other skills)

Skill	Role
/deep-research	This skill — 30–2 000 candidates (mode-dependent), top sources read, full report
/bear-hours	Frame a learning wedge (no reading)
/source-scout	5–7 reading picks in brief.md (no reading)

Do not auto-route here from other skills.

Hard rules

• Search wide before reading — log every candidate; never jump to 5 sources and call it done.
• Screening is mandatory — document exclusions with reason codes (see funnel reference).
• Read before summarizing — deep-read only eligible top picks; do not invent paper content.
• Synthesis cites only deep-read sources — cited count ≤ read count for the mode.
• Two artifacts — sources-index.md (full audit trail) + report.md (synthesis).
• Honest counts — if discovery < target for the mode, say so; never fake 200 screened.
• Own words — synthesize; no long copyrighted quotes (AGENTS.md).
• Report language — write report.md in the user's language; translate section headings if needed. Source titles stay in their original language.

Interactive questions

Use AskUserQuestion (or your environment's interactive question widget) for intake gates. If no widget exists, ask clearly in chat and wait for the answer.

Hard rules:

• Never list depth options as plain chat bullets — always use an interactive question (widget or explicit chat ask)
• One question per call — sharpen question and depth are separate calls
• STOP after each call; wait for the answer before continuing
• Do not start discovery (Step 2) until depth is confirmed
• extreme requires two confirmations — picker + dedicated cost gate (Step 0c)

Title format: Deep Research — {label}

Step 0: Intake

Input	Required?
Research question	Yes
Depth mode	Yes — via interactive question (unless smart-skipped)
Study link	Optional — studies/<slug>/brief.md

0a — Research question

Take the question from the user's message. If missing or too broad for one sentence → AskUserQuestion:

Title: Deep Research — Question

Ask: "Quelle question précise veux-tu que je réponde ? (une phrase, cadrée)"

Options: infer 2–3 sharpened variants from context, plus other — "Autre — je précise dans mon prochain message".

Derive <slug> from the question (lowercase, hyphens). Determine output path:

• If studies/<slug>/brief.md exists → studies/<slug>/research.md + studies/<slug>/sources-index.md
• Else → research/<slug>/report.md + research/<slug>/sources-index.md

0b — Existing folder (before any write)

Before creating or overwriting any file, check whether the target folder already has sources-index.md and/or report.md (or research.md).

Situation	Action
No existing index/report	Proceed to Step 0c (depth)
Index exists with pending rows	Propose resume — continue from first pending (screen/read) instead of restarting discovery
Index and/or report exist (recent)	Ask via interactive question: overwrite, resume, or extend — do not write until answered
User chose resume	Load existing index; skip discovery if all rows screened; jump to first incomplete stage
User chose extend	Keep existing index; append new discovery round (see escape hatches)
User chose overwrite	Proceed; replace files on first write

Fresh slug with no prior files → skip this gate.

0c — Depth level (mandatory gate)

Always call AskUserQuestion before Step 1 — unless smart-skipped (below).

Title: Deep Research — Profondeur

Ask: "Quel niveau de profondeur ? Ça fixe combien de sources je cherche, filtre et lis en profondeur."

Options (fixed — show all four with counts):

Option label	Mode ID
Quick — ~30–50 sources cherchées · 8–12 retenues au filtre · 2–3 lues · ~10 min	quick
Standard — ~80–120 cherchées · 25–40 retenues · 8–12 lues · ~20 min	standard
Literature review (recommandé) — 150–250+ cherchées · 50–80 retenues · 15–25 lues · ~40–60 min	literature-review
Extrême ⚠️ — ~2 000 cherchées · 20 sous-agents · 40–60 lues · coût tokens & temps élevés (~1–3 h)	extreme

If user picks extreme → STOP — go to Step 0d (do not confirm or start yet).

For quick / standard / literature-review, confirm in one line before Step 1, e.g.: Mode literature-review — je vise 150–250+ sources découvertes, 15–25 lectures en profondeur.

0d — Extreme confirmation (mandatory for extreme only)

Second gate — never skip. Call AskUserQuestion:

Title: Deep Research — Extrême ⚠️

Ask: "Mode extrême : ~2 000 sources via 20 sous-agents en parallèle (WebSearch massif). Coût estimé : 500k–2M+ tokens et 1–3 heures. Les APIs peuvent plafonner avant 2k — je rapporterai le compte réel. Tu confirmes ?"

Options:

• Oui — lancer le mode extrême (j'accepte tokens + temps)
• Non — revenir au choix de profondeur (Step 0c)

If Non → re-run Step 0c.

If Oui → confirm in one line, e.g.: Mode extreme confirmé — 20 sous-agents, cible ~2 000 sources découvertes, 40–60 lectures en profondeur.

Smart-skip (no depth question) only when the user already named a mode or time budget:

User said	Mode
quick, "rapide", "5 min", "10 min"	quick
standard, "moyen", "~20 min"	standard
literature-review, "recherche approfondie", "literature review", "complet", "full"	literature-review
extreme, "extrême", "2000", "2 000", "max depth"	extreme — still run Step 0d
/deep-research quick (mode in slash args)	matching mode

Not smart-skip: bare /deep-research, "vas-y", "go", "lance" without a mode → ask.

Extreme never smart-skips Step 0d — even if user said "extreme" upfront, always show the cost gate.

Depth modes reference (must match references/screening-funnel.md):

Mode	Discovered	Screened in	Read in depth	Cited in synthesis	Time hint
quick	30–50	8–12	2–3	≤2–3	~10 min
standard	80–120	25–40	8–12	≤8–12	~20 min
literature-review	150–250+	50–80	15–25	≤15–25	~40–60 min
extreme	~2 000	300–500	40–60	≤40–60	~1–3 h ⚠️

Step 1: Research plan

QUESTION: <one sentence>
SUB_QUESTIONS: <5–8 bullets>
INCLUSION: <what counts as on-topic>
EXCLUSION: <what to reject>
QUERY_ANGLES: <12–20 distinct angles for literature-review; 20 non-overlapping clusters for extreme>

Load references/screening-funnel.md, references/source-tiers.md, references/report-template.md.

For extreme also load references/extreme-orchestration.md and write research/<slug>/discovery/plan.md (20 angle clusters).

Step 2: Discover — cast the wide net

This step dominates. Do not proceed to deep reading until the discovery target is met or max rounds exhausted.

Skip if resume and discovery target already met in existing index.

Search rounds (literature-review)

Run 8–15 rounds of parallel WebSearch (4–5 queries per round). Each round uses new query angles from the plan — not repeats.

Rotate across:

Angle	Example
Survey / SOTA	"<topic>" systematic review
Mechanism	"<mechanism>" principle
Seminal	<founding author> <year>
Recent	<topic> 2024..2026
Venue	site:arxiv.org, site:ieee.org, conference name
Applied	case study deployment
Critique	limitations challenges
Adjacent	synonym terms, related subfields
Grey lit	technical reports, theses, industry whitepapers
FR/local	if question needs it

After each round: append new unique candidates to sources-index.md:

# Sources index — <slug>

**Question:** ...
**Mode:** literature-review
**Last updated:** <YYYY-MM-DD>

| # | Title | URL | Found via | Tier est. | Screen | Exclude reason |
|---|-------|-----|-----------|-----------|--------|----------------|
| 1 | ... | ... | survey query | 2 | pending | |

Dedup by URL / DOI / arXiv ID. Target: 150–250+ rows before screening.

quick / standard: fewer rounds per funnel table — same logging discipline.

Extreme — parallel sub-agent discovery

Only after Step 0d confirmed. Follow references/extreme-orchestration.md.

1. Create research/<slug>/discovery/ and discovery/plan.md (20 angle clusters)
2. Launch 20 sub-agents in one parallel batch via your environment's sub-agent/task mechanism; choose the fastest/most economical model available for discovery
3. Each agent targets ~100 candidates → discovery/shard-NN.md (WebSearch only, no WebFetch)
4. Merge all shards → sources-index.md + discovery/merge-log.md (global dedup, honest count)
5. If merged unique < 1 000 → tell user extreme target missed; offer extend or downgrade

Do not run extreme discovery single-threaded — the 20-agent fan-out is the point.

Step 3: Screen — title + abstract

Process every pending row in batches of 25–40. On resume, start at the first pending row.

1. Use snippet; WebFetch abstract only when title/snippet ambiguous
2. Set Screen: include or exclude + reason code (OFF_TOPIC, DUPLICATE, LOW_TIER, PAYWALL_NO_ALT, LANGUAGE, OUT_OF_DATE)
3. For include → assign tier estimate; promote best to eligible

Screen 60–80% out. Typical literature-review outcome: ~50–80 include from 200 discovered.

Extreme: launch up to 10 screening sub-agents in parallel (see extreme-orchestration.md); merge into sources-index.md. Target 300–500 include from ~2 000.

Update sources-index.md in place as you go.

Step 4: Rank eligible → select for deep read

Rank eligible sources (weights: answers question 35%, tier 25%, recency 15%, access 15%, non-redundancy 10%).

Promote top N to read per mode (15–25 for literature-review; 40–60 for extreme). Mark others eligible — not deep-read with one-line why.

Step 5: Read in depth

WebFetch each read source. Extract: thesis, methods, results, limitations.

Prefer arXiv / author PDF when paywalled. Skim abstracts only for eligible not promoted if they inform the funnel counts.

Read failure protocol

If WebFetch fails (403, paywall without alternative, unreadable PDF, timeout):

1. Mark the source read-failed in sources-index.md with a one-line reason
2. Promote the next eligible source to read to meet the mode's read target
3. Never summarize or cite a source not successfully read in depth

Context management (literature-review and above)

During Step 5, append structured notes as you read to research/<slug>/notes.md (or studies/<slug>/notes.md if study-linked):

## <Author year> — <short title>
- **Thesis:** ...
- **Methods:** ...
- **Results:** ...
- **Limits:** ...

Synthesize in Step 6 from this file — not from memory alone. For large read lists, batch reads via sub-agents is allowed if your environment supports it (same pattern as extreme discovery).

Step 6: Synthesize

Write report.md per references/report-template.md — in the user's language (translate template headings as needed).

• Screening funnel table with real counts from sources-index.md
• Executive summary — answer first
• Synthesis by theme — from read sources only (via notes.md)
• Exclusion summary — aggregate reason codes
• Pointer to full sources-index.md

If discovered < 150 in literature-review mode → ## Search coverage section: shortfall, untried angles, offer extend pass.

If extreme and discovered < 1 500 → ## Search coverage + ## Extreme run metadata per extreme-orchestration.md.

Step 7: Deliver

Tell the user:

1. Paths: report.md + sources-index.md (+ notes.md if written)
2. Funnel counts — discovered / screened / read / cited
3. Direct answer — 2–3 sentences
4. Best source to read first
5. Confidence — high | medium | low

If discovered < target: say how many more rounds would close the gap.

Suggest (do not auto-route): /layout-html for mise en page HTML — works on this report or any other text.

Escape hatches

User says	Action
quick / 5 min	Smart-skip depth ask → 30–50 discovered, 2–3 read
standard	Smart-skip depth ask → 80–120 discovered, 8–12 read
literature-review / "recherche approfondie"	Smart-skip depth ask → 150–250+ discovered, 15–25 read
extreme / "extrême"	Smart-skip depth ask → still require Step 0d → 20 agents, ~2k target
vas-y / go without mode	Ask depth via interactive question — do not default silently
resume	Load existing sources-index.md; continue at first pending or incomplete read; do not restart discovery
stop / arrête (extreme)	Halt sub-agents; merge partial index; report funnel so far
extend	Append new discovery round to existing sources-index.md, re-screen, update report
free only	Exclude paywalled without preprint
no file	Chat summary + funnel counts only

Self-check

• Overwrite/resume gate passed before first write (Step 0b)
• sources-index.md exists with actual discovered count
• Literature-review: ≥150 discovered OR shortfall documented
• Every exclude has a reason code
• Mode-appropriate deep-read count (15–25 literature-review; 40–60 extreme)
• Read failures marked read-failed; replacements promoted; no citation of unread sources
• Extreme: Step 0d confirmed; 20 shard files attempted; merge-log.md exists
• Extreme: never claim 2k discovered if merge count is lower
• Funnel table in report matches index counts; cited ≤ read
• Synthesis cites only deep-read sources
• Each SUB_QUESTION from Step 1 is addressed in synthesis or listed under Open questions
• notes.md written incrementally for literature-review+ before synthesis