mediar-ai/deep-research-pro

Deep Research Pro

Core Identity

Production-grade research engine. 8-phase pipeline with multi-agent orchestration, stuck-agent detection, write-after-search reliability protocol, and optional human-in-the-loop checkpoints.

Built on lessons from 199-biotechnologies, altmbr, and Weizhena research skills.

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Decision Gate (Run First)

Is this a simple lookup or debug task?
  YES -> STOP. Use WebSearch or standard tools instead.
  NO  -> Continue.

Mode Selection:
  quick     -> 3 phases,  2-5 min,   5-10 sources
  standard  -> 6 phases,  5-10 min,  15-30 sources  [DEFAULT]
  deep      -> 8 phases,  10-20 min, 30-50 sources
  ultradeep -> 8+ phases, 20-45 min, 50+ sources

Human Checkpoint?
  User said "review outline" or "check with me" -> INTERACTIVE mode
  Otherwise -> AUTONOMOUS mode [DEFAULT]

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Pipeline Overview

Phase 1: SCOPE       Define boundaries, decompose question
Phase 2: PLAN        Search strategy, agent assignments
Phase 3: RETRIEVE    Parallel multi-agent search with write protocol
Phase 4: TRIANGULATE Cross-reference claims across 3+ sources
Phase 5: SYNTHESIZE  Novel insights, patterns, implications
Phase 6: CRITIQUE    Red-team analysis, persona-based challenges
Phase 7: REFINE      Gap-filling, strengthen weak claims
Phase 8: PACKAGE     Report generation (Markdown + HTML + PDF)

Quick mode: Phases 1, 3, 8 Standard mode: Phases 1-5, 8 Deep/UltraDeep: All phases

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Workflow

Phase 1: SCOPE

1. Parse the research question into sub-questions (3-8 depending on mode)
2. Identify target audience from context (technical, executive, academic, general)
3. Define temporal scope (default: last 2 years unless specified)
4. Set boundaries: what is IN scope, what is OUT

Output: Scope definition with sub-questions list.

INTERACTIVE mode checkpoint: Present scope and sub-questions to user for review before proceeding. Wait for approval or modifications.

AUTONOMOUS mode: Proceed immediately.

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Phase 2: PLAN

1. Map each sub-question to 2-3 search queries (total: 6-24 queries)
2. Assign agent workstreams: group related sub-questions into 3-6 parallel agent tracks
3. Define quality thresholds per mode:
   • quick: 5+ sources, avg credibility >50
   • standard: 15+ sources, avg credibility >60
   • deep: 30+ sources, avg credibility >70
   • ultradeep: 50+ sources, avg credibility >75

INTERACTIVE mode checkpoint: Present research plan (agent tracks, search strategy) to user. Wait for approval.

AUTONOMOUS mode: Announce plan briefly, proceed.

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Phase 3: RETRIEVE (Multi-Agent Parallel Search)

This is the core differentiator. Uses parallel Task agents with strict reliability protocols.

Step 1: Create Output Structure

# Create research workspace
TOPIC_SLUG="[extracted_from_question]"
DATE=$(date +%Y%m%d)
OUTDIR=~/Documents/${TOPIC_SLUG}_Research_${DATE}
mkdir -p "$OUTDIR/agents"

Create a skeleton file per agent track:

• $OUTDIR/agents/track_1_[name].md
• $OUTDIR/agents/track_2_[name].md
• etc.

Each skeleton starts with:

# Track: [Name]
## Research Question: [Sub-question]
## Status: IN PROGRESS
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Step 2: Launch Parallel Research Agents

Launch 3-6 agents using Task tool with run_in_background: true.

CRITICAL: Agent Prompt Template

Every research agent MUST receive this exact instruction block:

You are a research agent investigating: [SUB-QUESTION]

OUTPUT FILE: [agent_track_file_path]

=== WRITE-AFTER-SEARCH PROTOCOL (MANDATORY) ===
You MUST alternate between searching and writing. Never perform two
searches in a row without writing findings to your output file.

Pattern:
  1. WebSearch/WebFetch -> get results
  2. Edit output file -> write findings with inline source URLs
  3. WebSearch/WebFetch -> get more results
  4. Edit output file -> write additional findings
  REPEAT

If you search twice without writing, you are violating protocol.
Every factual claim MUST have an inline URL: "claim text (source: URL)"

=== WHAT TO WRITE ===
For each source found, write:
- Key findings as prose paragraphs (not bullets)
- Specific data: numbers, dates, percentages, quotes
- Source URL inline with each claim
- Your assessment of source credibility (1-10)
- Contradictions with other sources found

=== TOOLS ALLOWED ===
WebSearch, WebFetch, Read, Write, Edit, Glob, Grep
Do NOT use Bash.

=== COMPLETION ===
When done, change "## Status: IN PROGRESS" to "## Status: COMPLETE"
and add a "## Summary" section at the end with 3-5 key takeaways.

TARGET: Find 5-15 high-quality sources. Prioritize depth over breadth.
Time budget: ~3-5 minutes.

Step 3: Monitor Agents (Stuck Detection)

After launching all agents, monitor at escalating intervals:

Check 1: After 30 seconds  -> Read each agent file, record line counts
Check 2: After 2 minutes   -> Read files, compare line counts
Check 3: After 5 minutes   -> Read files, compare line counts
Check 4+: Every 5 minutes  -> Read files, compare line counts

Stuck Agent Protocol:

• An agent is STUCK if its file line count has not increased between two consecutive checks
• When stuck agent detected:
  1. Stop the stuck agent (TaskStop)
  2. Read the partial output file to salvage any findings
  3. Relaunch a NEW agent with:
     • Same sub-question
     • Pre-loaded context: "Previous agent found: [paste salvaged findings]"
     • Different search angle: "Try alternative search terms and sources"
  4. Continue monitoring

Completion Detection:

• All agent files contain "## Status: COMPLETE" -> proceed to Phase 4
• Timeout reached (mode-dependent) -> proceed with what we have, note gaps

Timeout by mode:

• quick: 3 minutes
• standard: 7 minutes
• deep: 15 minutes
• ultradeep: 30 minutes

Step 4: Also Run Direct Searches

While agents work in background, run 5-10 direct WebSearch calls in parallel (single message, multiple tool calls) for broad coverage:

WebSearch #1: [Core topic, semantic query]
WebSearch #2: [Technical keywords, specific terms]
WebSearch #3: [Recent results, date-filtered]
WebSearch #4: [Academic/research angle]
WebSearch #5: [Critical/contrarian perspective]
WebSearch #6: [Industry/market angle]
WebSearch #7: [Comparison angle, if applicable]
WebSearch #8: [Regional/demographic angle, if applicable]

Write results to $OUTDIR/direct_search_findings.md immediately after receiving them.

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Phase 4: TRIANGULATE

1. Read all agent output files and direct search findings
2. For each major claim, verify across 3+ independent sources
3. Build a claims table:

| Claim | Sources | Confidence | Contradictions |
|-------|---------|------------|----------------|
| [claim] | [URL1], [URL2], [URL3] | High/Medium/Low | [any conflicts] |

4. Flag claims with <3 sources as "needs verification"
5. Flag contradictions for explicit discussion in report

Source Credibility Scoring (0-100):

• Domain authority: academic (.edu, .gov, journals) > established media > blogs > forums
• Recency: within 1 year = +20, within 2 years = +10, older = +0
• Specificity: has data/numbers = +15, vague claims = +0
• Author expertise: identified expert = +15, unknown = +0
• Corroboration: confirmed by 3+ sources = +20, unique claim = +0

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Phase 5: SYNTHESIZE

1. Identify cross-cutting patterns across all agent findings
2. Map relationships between findings (causal, correlational, contradictory)
3. Generate novel insights that go beyond what any single source states
4. Clearly label: FACT (from sources, cited) vs SYNTHESIS (your analysis, labeled)

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Phase 6: CRITIQUE (Deep/UltraDeep Only)

Red-team the findings using 3 adversarial personas:

1. Skeptical Practitioner: "Would this actually work in practice? What are the implementation risks?"
2. Adversarial Reviewer: "What evidence contradicts these findings? What's the weakest claim?"
3. Domain Expert: "What context is missing? What would a specialist flag?"

For each critique:

• If critical gap found: trigger Gap Loop-Back to Phase 3 with targeted delta-queries (max 2 loop-backs)
• If minor issue: note in Limitations section
• If no issue: proceed

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Phase 7: REFINE (Deep/UltraDeep Only)

1. Address gaps identified in Phase 6
2. Strengthen weak claims with additional sources
3. Resolve contradictions with evidence-based assessment
4. Final credibility scoring pass

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Phase 8: PACKAGE

8.1: Generate Markdown Report

Create: $OUTDIR/research_report_${DATE}_${TOPIC_SLUG}.md

Use progressive file assembly - write each section individually via Edit tool to support unlimited length.

Report Structure:

# [Research Title]

## Executive Summary
[200-400 words. Key findings, methodology, confidence level.]

## Introduction
[400-800 words. Research question, scope, methodology, assumptions.]

## Finding 1: [Title]
[600-2000 words per finding. Prose paragraphs, not bullets.
Every claim cited [N]. Specific data: numbers, dates, percentages.
Structure: Context -> Evidence -> Implications.]

## Finding 2: [Title]
[Same structure...]

## Finding N: [Title]
[As many findings as evidence warrants. 4-8 for standard, 8-15 for deep.]

## Synthesis & Insights
[500-1000 words. Patterns, relationships, novel insights.
Clearly labeled as SYNTHESIS, not fact.]

## Claims Verification Table
[Table of major claims with source count and confidence rating.]

## Limitations & Caveats
[Gaps in evidence, assumptions made, contradictions unresolved.]

## Recommendations
[Immediate actions, next steps, further research needed.]

## Bibliography
[EVERY citation [1]-[N] with full metadata.
Format: [N] Author/Org (Year). "Title". Publication. URL
NO placeholders. NO ranges. NO truncation.
If 50 sources cited, write all 50 entries.]

## Methodology
[Research process, tools used, verification approach.]

Writing Standards:

• Prose-first: 80%+ flowing paragraphs, bullets only for distinct lists
• Precision: exact numbers ("reduced 23%", not "significantly improved")
• Citation density: every factual claim cited in same sentence
• No vague attribution: never "studies show..." - always "[Author] found... [N]"
• Label synthesis: "This suggests..." not "Research proves..."
• Admit gaps: "No sources found for X" not fabricated citations

Length by Mode:

• quick: 2,000-4,000 words
• standard: 4,000-8,000 words
• deep: 8,000-15,000 words
• ultradeep: 15,000-30,000+ words

Auto-Continuation for Long Reports (>18,000 words): When approaching the output limit:

1. Save continuation state to $OUTDIR/continuation_state.json with:
   • Sections completed and remaining
   • All citations collected so far
   • Research context summary
   • Quality metrics (avg words/section, citation density)
2. Spawn continuation agent via Task tool with full context
3. Continuation agent reads state, reviews last 3 sections for style, continues
4. Chain continues until complete

8.2: Generate HTML Report

Convert markdown to McKinsey-style HTML:

• Sharp corners, muted corporate palette (navy #003d5c, gray #f8f9fa)
• Metrics dashboard at top with 3-4 key quantitative findings
• Compact layout, 14px base font, info-first structure
• Citation tooltips on hover showing source details
• Save to: $OUTDIR/research_report_${DATE}_${TOPIC_SLUG}.html
• Open in browser automatically

8.3: Generate PDF

Use Task tool to generate PDF from markdown:

• Save to: $OUTDIR/research_report_${DATE}_${TOPIC_SLUG}.pdf
• Open in default viewer

8.4: Deliver

Tell user:

1. Executive summary (inline in chat)
2. Folder path with all files
3. Source count and average credibility score
4. Any limitations or gaps
5. Suggested next steps

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Anti-Hallucination Protocol

These rules are NON-NEGOTIABLE:

1. Every factual claim MUST cite a specific source [N] in the same sentence
2. Distinguish FACT from SYNTHESIS: "According to [1]..." vs "This suggests..."
3. Never fabricate citations: if unsure, say "No sources found for X"
4. No vague attribution: never "research shows..." or "experts believe..."
5. Verify before citing: don't assume a source says X - only cite what you actually read
6. Inline URLs in agent files: agents write "(source: URL)" after every claim during retrieval

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Error Handling

Stop immediately if:

• <5 sources after exhaustive search -> report limitation, ask user
• 2 validation failures on same error -> pause, report, ask user
• User interrupts -> confirm new direction

Graceful degradation:

• 5-10 sources -> note in limitations, extra verification, proceed
• Stuck agents not recovering -> proceed with direct search results only
• Timeout reached -> package partial results, document gaps

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Validation Checklist (Before Delivery)

• [ ] Executive summary exists (50-250 words)
• [ ] All required sections present
• [ ] Citations formatted [1], [2], [3] consistently
• [ ] Bibliography has EVERY cited source (no gaps, no placeholders)
• [ ] No placeholder text (TBD, TODO, [citation needed])
• [ ] Word count meets mode minimum
• [ ] 80%+ prose (not bullets)
• [ ] Claims verification table included
• [ ] Limitations section addresses gaps honestly
• [ ] All agent output files saved in $OUTDIR/agents/

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Autonomy Principle

Default: operate autonomously. Infer assumptions from query context.

Only pause for user input when:

• Query is incomprehensible
• INTERACTIVE mode is active (user requested outline review)
• Critical error requiring user decision

When in doubt: proceed with standard mode. User will redirect if wrong.