feat(skills): add deep-research skill

Copy deep-research skill from local Qoder installation to config repo for version control

skills/deep-research/references/systematic_review_protocol.md

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+# Systematic Review Mode — Full Protocol
+
+Full PRISMA-compliant systematic literature review with optional meta-analysis. This mode extends the standard 6-phase pipeline with specialized agents for risk of bias assessment (RoB 2, ROBINS-I) and quantitative synthesis.
+
+See `agents/risk_of_bias_agent.md` and `agents/meta_analysis_agent.md` for detailed agent definitions.
+See `references/systematic_review_toolkit.md` for the Cochrane/PRISMA/GRADE reference guide.
+
+## 5-Phase Pipeline
+
+```
+User: "Systematic review of [topic]" / "Meta-analysis of [topic]"
+     |
+=== Phase 1: SCOPING (Generates Protocol, not just RQ) ===
+     |
+     |-> [research_question_agent] -> PICOS-formatted RQ
+     |   - Population, Intervention, Comparator, Outcome, Study design
+     |   - Explicit eligibility criteria (inclusion/exclusion)
+     |
+     |-> [research_architect_agent] -> Systematic Review Protocol
+     |   - Protocol follows PRISMA-P 2015 (templates/prisma_protocol_template.md)
+     |   - Pre-specified subgroup analyses and sensitivity analyses
+     |   - Risk of bias tool selection (RoB 2 / ROBINS-I)
+     |   - Meta-analysis feasibility pre-assessment
+     |
+     +-> [devils_advocate_agent] -- CHECKPOINT 1
+         - PICOS specificity check
+         - Search strategy comprehensiveness
+         - Protocol completeness
+         - Verdict: PASS / REVISE
+     |
+     ** User confirmation of protocol before Phase 2 **
+     |
+=== Phase 2: INVESTIGATION (PRISMA-Compliant Search + RoB) ===
+     |
+     |-> [bibliography_agent] -> PRISMA Flow Diagram + Source Corpus
+     |   - Search >= 2 databases with documented strategy
+     |   - Dual-pass screening (title/abstract -> full text)
+     |   - PRISMA 2020 flow diagram with counts at each stage
+     |   - Excluded studies with reasons documented
+     |
+     |-> [source_verification_agent] -> Verified Sources
+     |   - Standard verification + predatory journal screening
+     |
+     +-> [risk_of_bias_agent] -> RoB Assessment
+         - Per-study domain assessment with signaling questions
+         - Traffic-light summary table across all studies
+         - Distribution summary (% Low / Some Concerns / High)
+     |
+=== Phase 3: ANALYSIS (Meta-Analysis or Narrative Synthesis) ===
+     |
+     |-> [meta_analysis_agent] -> Quantitative or Narrative Synthesis
+     |   - Feasibility assessment (pool or not?)
+     |   - If feasible: effect size calculation, forest plot data,
+     |     heterogeneity (I-squared, Q, tau-squared), subgroup/sensitivity analyses
+     |   - If not feasible: structured narrative synthesis (SWiM)
+     |   - GRADE certainty of evidence for each outcome
+     |
+     |-> [synthesis_agent] -> Qualitative Themes + Gap Analysis
+     |   - Thematic synthesis across studies
+     |   - Integration with quantitative findings
+     |
+     +-> [devils_advocate_agent] -- CHECKPOINT 2
+         - Cherry-picking check
+         - Heterogeneity explanation adequacy
+         - GRADE assessment validity
+         - Verdict: PASS / REVISE
+     |
+=== Phase 4: COMPOSITION ===
+     |
+     +-> [report_compiler_agent] -> PRISMA 2020 Report
+         - Uses templates/prisma_report_template.md
+         - All 27 PRISMA items mapped to sections
+         - Study characteristics table
+         - Risk of bias summary table
+         - Forest plot data (if meta-analysis)
+         - GRADE Summary of Findings table
+     |
+=== Phase 5: REVIEW (Parallel) ===
+     |
+     |-> [editor_in_chief_agent] -> Editorial Verdict
+     |-> [ethics_review_agent] -> Ethics Clearance
+     +-> [devils_advocate_agent] -- CHECKPOINT 3
+     |
+=== Phase 6: REVISION ===
+     |
+     +-> [report_compiler_agent] -> Final PRISMA Report
+```
+
+## Checkpoint Rules
+
+1. All standard checkpoint rules apply (see SKILL.md Checkpoint Rules)
+2. **Protocol must be registered** (or registration recommended) before Phase 2
+3. **Risk of bias must be completed for all studies** before Phase 3
+4. **GRADE assessment required** for every pooled outcome
+5. **PRISMA checklist compliance** verified in Phase 5