name: "Deep Research Kitty"
description: "Conduct systematic research with structured methodology and evidence synthesis"
version: "1.0.0"
domain: "research"

# Workflow customization
workflow:
  phases:
    - name: "question"
      description: "Define research question and scope"
    - name: "methodology"
      description: "Design research methodology"
    - name: "gather"
      description: "Collect data and sources"
    - name: "analyze"
      description: "Analyze findings"
    - name: "synthesize"
      description: "Synthesize results and draw conclusions"
    - name: "publish"
      description: "Prepare findings for publication"

# Expected artifacts
artifacts:
  required:
    - spec.md              # Research question and scope
    - plan.md              # Methodology plan
    - tasks.md             # Research work packages
    - findings.md          # Synthesized findings
  optional:
    - sources/             # Source documents
    - data/                # Raw data
    - analysis/            # Analysis outputs
    - literature-review.md # Optional extended literature review
    - methodology.md       # Detailed methodology appendix
    - synthesis.md         # Synthesis notes or drafts

# Path conventions for this mission
paths:
  workspace: "research/"
  data: "data/"
  deliverables: "findings/"
  documentation: "reports/"

# Validation rules
validation:
  checks:
    - all_sources_documented
    - methodology_clear
    - findings_synthesized
    - no_unresolved_questions
  custom_validators: true  # Use validators.py

# MCP tools recommended for this mission
mcp_tools:
  required:
    - filesystem
    - git
  recommended:
    - web-search
    - pdf-reader
    - citation-manager
    - arxiv-search
  optional:
    - data-analysis
    - statistics
    - pubmed-search

# Agent personality/instructions
agent_context: |
  You are a research agent conducting systematic literature reviews and empirical research.
  Your mission is to maintain research integrity and methodological rigor throughout every phase.

  Key Practices:
  - Document ALL sources in research/source-register.csv with proper citations, URLs, and access dates.
  - Extract findings to research/evidence-log.csv with confidence levels (high/medium/low) and contextual notes.
  - Clearly articulate methodology decisions for reproducibility and peer review.
  - Distinguish raw evidence from interpretation; cite every claim.
  - Identify limitations, threats to validity, and alternative explanations.
  - Synthesize findings so that each conclusion traces back to documented evidence rows.

  Citation Standards:
  - Use BibTeX or APA format (include DOI or URL when available).
  - Track access dates for all online sources.
  - Assign confidence levels commensurate with source quality.

  Workflow Phases: question → methodology → gather → analyze → synthesize → publish.

# Task metadata fields
task_metadata:
  required:
    - task_id
    - lane
    - phase
    - agent
  optional:
    - shell_pid
    - assignee
    - estimated_hours
    - experiment_id
    - data_collection_round

# Command customization
commands:
  specify:
    prompt: "Define research question, scope, and expected outcomes"
  plan:
    prompt: "Design research methodology and data collection strategy"
  tasks:
    prompt: "Break into research work packages (literature review, data collection, analysis)"
  implement:
    prompt: "Execute research plan and collect findings"
  review:
    prompt: "Review findings for validity, completeness, and proper documentation"
  accept:
    prompt: "Validate research completeness and readiness for publication"
