Deep Research

Core System Instructions

Purpose: Deliver citation-backed, verified research reports through 8-phase pipeline (Scope → Plan → Retrieve → Triangulate → Synthesize → Critique → Refine → Package) with source credibility scoring and progressive context management.

Context Strategy: This skill uses 2025 context engineering best practices:

• Static instructions cached (this section)
• Progressive disclosure (load references only when needed)
• Avoid "loss in the middle" (critical info at start/end, not buried)
• Explicit section markers for context navigation

Decision Tree (Execute First)

Request Analysis
├─ Simple lookup? → STOP: Use WebSearch, not this skill
├─ Debugging? → STOP: Use standard tools, not this skill
└─ Complex analysis needed? → CONTINUE

Mode Selection
├─ Initial exploration? → quick (3 phases, 2-5 min)
├─ Standard research? → standard (6 phases, 5-10 min) [DEFAULT]
├─ Critical decision? → deep (8 phases, 10-20 min)
└─ Comprehensive review? → ultradeep (8+ phases, 20-45 min)

Execution Loop (per phase)
├─ Load phase instructions from [methodology](./reference/methodology.md#phase-N)
├─ Execute phase tasks
├─ Spawn parallel agents if applicable
└─ Update progress

Validation Gate
├─ Run `python scripts/validate_report.py --report [path]`
├─ Pass? → Deliver
└─ Fail? → Fix (max 2 attempts) → Still fails? → Escalate

Workflow (Clarify → Plan → Act → Verify → Report)

AUTONOMY PRINCIPLE: This skill operates independently. Infer assumptions from query context. Only stop for critical errors or incomprehensible queries.

1. Clarify (Rarely Needed - Prefer Autonomy)

DEFAULT: Proceed autonomously. Derive assumptions from query signals.

ONLY ask if CRITICALLY ambiguous:

• Query is incomprehensible (e.g., "research the thing")
• Contradictory requirements (e.g., "quick 50-source ultradeep analysis")

When in doubt: PROCEED with standard mode. User will redirect if incorrect.

Default assumptions:

• Technical query → Assume technical audience
• Comparison query → Assume balanced perspective needed
• Trend query → Assume recent 1-2 years unless specified
• Standard mode is default for most queries

2. Plan

Mode selection criteria:

• Quick (2-5 min): Exploration, broad overview, time-sensitive
• Standard (5-10 min): Most use cases, balanced depth/speed [DEFAULT]
• Deep (10-20 min): Important decisions, need thorough verification
• UltraDeep (20-45 min): Critical analysis, maximum rigor

Announce plan and execute:

• Briefly state: selected mode, estimated time, number of sources
• Example: "Starting standard mode research (5-10 min, 15-30 sources)"
• Proceed without waiting for approval

3. Act (Phase Execution)

All modes execute:

• Phase 1: SCOPE - Define boundaries (method)
• Phase 3: RETRIEVE - Parallel search execution (5-10 concurrent searches + agents) (method)
• Phase 8: PACKAGE - Generate report using template

Standard/Deep/UltraDeep execute:

• Phase 2: PLAN - Strategy formulation
• Phase 4: TRIANGULATE - Verify 3+ sources per claim
• Phase 4.5: OUTLINE REFINEMENT - Adapt structure based on evidence (WebWeaver 2025) (method)
• Phase 5: SYNTHESIZE - Generate novel insights

Deep/UltraDeep execute:

• Phase 6: CRITIQUE - Red-team analysis
• Phase 7: REFINE - Address gaps

Critical: Avoid "Loss in the Middle"

• Place key findings at START and END of sections, not buried
• Use explicit headers and markers
• Structure: Summary → Details → Conclusion (not Details sandwiched)

Progressive Context Loading:

• Load methodology sections on-demand
• Load template only for Phase 8
• Do not inline everything - reference external files

Anti-Hallucination Protocol (CRITICAL):

• Source grounding: Every factual claim MUST cite a specific source immediately [N]
• Clear boundaries: Distinguish between FACTS (from sources) and SYNTHESIS (your analysis)
• Explicit markers: Use "According to [1]..." or "[1] reports..." for source-grounded statements
• No speculation without labeling: Mark inferences as "This suggests..." not "Research shows..."
• Verify before citing: If unsure whether source actually says X, do NOT fabricate citation
• When uncertain: Say "No sources found for X" rather than inventing references

Parallel Execution Requirements (CRITICAL for Speed):

Phase 3 RETRIEVE - Mandatory Parallel Search:

1. Decompose query into 5-10 independent search angles before ANY searches
2. Launch ALL searches in single message with multiple tool calls (NOT sequential)
3. Quality threshold monitoring for FFS pattern:
   • Track source count and avg credibility score
   • Proceed when threshold reached (mode-specific, see methodology)
   • Continue background searches for additional depth
4. Spawn 3-5 parallel agents using Task tool for deep-dive investigations

Example correct execution:

[Single message with 8+ parallel tool calls]
WebSearch #1: Core topic semantic
WebSearch #2: Technical keywords
WebSearch #3: Recent 2024-2025 filtered
WebSearch #4: Academic domains
WebSearch #5: Critical analysis
WebSearch #6: Industry trends
Task agent #1: Academic paper analysis
Task agent #2: Technical documentation deep dive

❌ WRONG (sequential execution):

WebSearch #1 → wait for results → WebSearch #2 → wait → WebSearch #3...

✅ RIGHT (parallel execution):

All searches + agents launched simultaneously in one message

4. Verify (Always Execute)

Step 1: Citation Verification (Catches Fabricated Sources)

python scripts/verify_citations.py --report [path]

Checks:

• DOI resolution (verifies citation actually exists)
• Title/year matching (detects mismatched metadata)
• Flags suspicious entries (2024+ without DOI, no URL, failed verification)

If suspicious citations found:

• Review flagged entries manually
• Remove or replace fabricated sources
• Re-run until clean

Step 2: Structure & Quality Validation

python scripts/validate_report.py --report [path]

8 automated checks:

1. Executive summary length (50-250 words)
2. Required sections present (+ recommended: Claims table, Counterevidence)
3. Citations formatted [1], [2], [3]
4. Bibliography matches citations
5. No placeholder text (TBD, TODO)
6. Word count reasonable (500-10000)
7. Minimum 10 sources
8. No broken internal links

If fails:

• Attempt 1: Auto-fix formatting/links
• Attempt 2: Manual review + correction
• After 2 failures: STOP → Report issues → Ask user

5. Report

CRITICAL: Generate COMPREHENSIVE, DETAILED markdown reports

File Organization (CRITICAL - Clean Accessibility):

1. Create Organized Folder in Documents:

• ALWAYS create dedicated folder: ~/Documents/[TopicName]_Research_[YYYYMMDD]/
• Extract clean topic name from research question (remove special chars, use underscores/CamelCase)
• Examples:
  • "psilocybin research 2025" → ~/Documents/Psilocybin_Research_20251104/
  • "compare React vs Vue" → ~/Documents/React_vs_Vue_Research_20251104/
  • "AI safety trends" → ~/Documents/AI_Safety_Trends_Research_20251104/
• If folder exists, use it; if not, create it
• This ensures clean organization and easy accessibility

2. Save All Formats to Same Folder:

Markdown (Primary Source):

• Save to: [Documents folder]/research_report_[YYYYMMDD]_[topic_slug].md
• Al