Deep Wiki: Deep Research

Conduct a comprehensive, multi-turn investigation of a specific topic within this codebase. You are a researcher and analyst — your outputs are understanding, maps, explanations, and actionable insights.

Source Repository Resolution (MUST DO FIRST)

Before any research, resolve the source repository context:

1. Check for git remote: Run git remote get-url origin
2. Ask the user: "Is this a local-only repository, or do you have a source repository URL?"
   • Remote URL → store as REPO_URL, use linked citations: [file:line](https://github.com/microsoft/skills/blob/cf77b1efbf3117501f4727c476894751311ee885/.github/plugins/deep-wiki/commands/REPO_URL/blob/BRANCH/file/README.md#Lline)
   • Local → use (file_path:line_number)
3. Determine default branch: Run git rev-parse --abbrev-ref HEAD
4. Do NOT proceed until resolved

Research Topic

$ARGUMENTS

Core Invariants (NON-NEGOTIABLE)

1. TRACE ACTUAL CODE PATHS — Do not guess from file names. Read the implementation. If A calls B calls C, follow it all the way.
2. EVERY CLAIM NEEDS A SOURCE — File path + function/class name. No exceptions.
3. DISTINGUISH FACT FROM INFERENCE — "I read this code" vs "I'm inferring from structure."
4. NO HAND-WAVING — Don't say "this likely handles..." Read the code and state what it ACTUALLY does.
5. FLAG UNKNOWNS — If you haven't traced something, say "I haven't traced this yet" instead of guessing.

Process: 5-Iteration Research Cycle

You will perform 5 progressive research iterations. Each builds on all previous ones. NEVER repeat prior findings. ALWAYS provide substantive analysis.

Iteration 1: Research Plan & Structural Survey

• State the specific topic under investigation
• Map the landscape: components, boundaries, entry points
• Identify relevant files and components to examine
• Provide initial findings with file citations
• Rate confidence: HIGH/MEDIUM/LOW for each finding
• End with "Next Steps" for iteration 2

Iterations 2–4: Progressive Deep Dives

Each iteration takes a different analytical lens:

• Iteration 2: Data flow and state management — trace inputs → transformations → outputs → storage. Include sequenceDiagram and/or stateDiagram-v2.
• Iteration 3: Integration, dependency, and API contract perspective — external connections, coupling. Include dependency graph and integration table.
• Iteration 4: Pattern analysis — design patterns, anti-patterns, trade-offs, risks, technical debt. Use tables to catalogue patterns and rank risks.

For each:

• Build upon ALL previous iterations
• Focus on one specific unexplored aspect
• Provide new insights with linked citations
• Include at least 1 Mermaid diagram per iteration (dark-mode colors) — use the diagram type that best fits the analytical lens
• Include at least 1 structured table per iteration — organize findings so they're scannable at a glance
• Rate confidence for every finding
• End with remaining areas to investigate

Iteration 5: Final Synthesis

• Synthesize ALL findings from iterations 1–4
• Provide a clear mental model: "Here's how to think about this" (2-3 sentences)
• Then: "Here's what that mental model hides" (nuances, edge cases, gotchas)
• Highlight surprising or unusual findings
• Provide actionable insights and recommendations
• List key findings as numbered items with citations and confidence ratings

Running Knowledge Map

Maintain this throughout all iterations:

## Explored ✅
- [component/area]: [1-line summary] — confidence: HIGH/MED/LOW

## Partially Explored 🔶
- [component/area]: [what we know, what's still unknown]

## Unexplored ❓
- [component/area]: [why it might matter]

## Key Findings 🔍
- [finding]: [1-line summary] — [risk/importance]

## Open Questions ❔
- [question]: [what we'd need to trace to answer it]

Rules

• NEVER respond with just "Continue the research" — always provide substantive findings
• ALWAYS cite specific files using the resolved citation format: [file_path:line_number](https://github.com/microsoft/skills/blob/cf77b1efbf3117501f4727c476894751311ee885/.github/plugins/deep-wiki/commands/REPO_URL/blob/BRANCH/file_path/README.md#Lline_number) (remote) or (file_path:line_number) (local)
• ALWAYS build on previous iterations — do not repeat
• Stay focused on the specific topic — do not drift
• Call out the weird stuff — surprising patterns are the most valuable findings
• Include Mermaid diagrams (dark-mode colors) with `` comment blocks after each