Exhaustive investigation with citations and structured findings. Use when thorough coverage is needed, all sources must be cited, or research will inform critical decisions. Triggers on: 'use deep-research mode', 'deep research', 'exhaustive investigation', 'thorough research', 'cite all sources', 'comprehensive analysis', 'leave no stone unturned', 'research everything'. Read-only mode - investigates and documents but doesn't modify code.
Exhaustive investigation with full citations and structured findings.
"Thorough beats fast. Citations beat claims. Structured beats stream-of-consciousness."
This mode is for when surface-level understanding isn't enough. You're building a complete, citable reference that others can verify.
Every deep-research output must include:
2-3 sentences covering:
| Included | Excluded |
|---|---|
| [What was researched] | [What was intentionally skipped] |
Each finding must have:
#### Finding: [Title]
**Confidence:** High | Medium | Low
**Evidence:**
- [file.py#L42](file.py#L42) - [what this shows]
- [config.yaml#L15](config.yaml#L15) - [what this shows]
**Analysis:**
[Interpretation of the evidence]
**Implications:**
[What this means for the task at hand]
| Area | Files Checked | Confidence |
|---|---|---|
| [Component A] | 12 | High |
| [Component B] | 5 | Medium |
| [Component C] | 0 | Not investigated |
Before going deep, establish the landscape:
For each important area:
Connect findings across areas:
[path/to/file.py#L42-L50](path/to/file.py#L42-L50) - Description
| Level | Meaning | Citation Requirement |
|---|---|---|
| High | Verified in code, tests pass | Direct code citation |
| Medium | Inferred from patterns | Multiple supporting citations |
| Low | Speculation based on naming/structure | Clearly marked as inference |
Before completing research:
| ❌ Don't | ✅ Do |
|---|---|
| "The codebase uses React" | "package.json#L15 lists [email protected] as dependency" |
| "This probably handles auth" | "Auth handling uncertain - no direct evidence found (Low confidence)" |
| "I looked at the files" | "Examined 23 files in src/services/, found 4 relevant" |
| "Everything seems fine" | "No issues found in [scope]. Coverage: [X] files, [Y] functions" |
When spawned as a subagent from Explorer: