# Investigate > Deep root cause analysis engine for defects whose cause is genuinely unknown. Runs an 8-phase diagnostic protocol — observe, reproduce, trace, hypothesize, prove, root cause, fix, prevent — using sequential-thinking MCP, multi-pass code reading, git forensics, competing hypotheses, and the 5 Whys, proving the cause with evidence before any fix. Returns a proven root-cause report; the fix runs only after that diagnosis is approved. Use when the user runs /investigate, or when a bug, crash, exception, stack trace, regression, flaky or intermittent failure, data corruption, memory leak, or unexplained slowness needs its root cause found and nobody knows why. Expensive — do not select it when the cause is already known, for a typo, syntax, import or config mistake, for a feature request or refactor, for "what does this code do", or for applying a fix the user already chose; handle those directly. For a live production outage, route to incident-commander first and investigate after service is restored. - Skill: `pfangueiro/investigate` (Agent Skill, multi-file: 2 files) - Install (CLI): `npx skillmds@latest add pfangueiro/investigate` - Raw SKILL.md: https://api.skillmd.com/api/skills/pfangueiro/investigate/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: AI & ML - Author: pfangueiro (https://skillmd.com/u/pfangueiro) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/pfangueiro/investigate --- # Investigate — Root Cause Analysis Engine Systematic deep investigation protocol. Finds the REAL cause, not the surface symptom. **Core principle:** Never fix what you don't understand. Every fix must trace to a proven root cause with evidence. ## Pre-Flight Gate Activation is decided by the frontmatter description alone — this file is read only AFTER the skill has been selected. Nothing here can prevent over-triggering, so this gate is a **post-selection redirect**, not a filter. **Before proceeding, check the ABORT and ROUTE OUT conditions below. If any holds, STOP, say in one line which one fired, and take the redirect instead of starting the 8-phase protocol.** Being invoked — including a literal `/investigate` or "find the root cause" — does NOT override an ABORT: the phrasing that selected this skill is not evidence the cause is unknown. - Run the 8-phase protocol only for a real bug / unexpected behavior whose root cause is UNKNOWN. - ABORT: a bug whose cause is already known (just fix it), a feature request, an obvious-cause config/syntax error, or anything not actually broken. - ROUTE OUT: a **live production outage** — service down, users impacted, an active incident — goes to **incident-commander FIRST**. Mitigate and restore service, then run `/investigate` for the root cause. An unknown cause does NOT admit an outage to this protocol: diagnosis-before-mitigation is paid for in downtime. ## Protocol Process every `/investigate` invocation through these 8 phases in strict order. Never skip a phase. Never jump to Phase 7 (FIX) without completing Phases 1-6 **and** satisfying the Phase 6 consent gate. Phase 6 is a hard halt: stopping there for approval is a correct completion of the protocol, not a skipped phase. --- ### Phase 1: OBSERVE — Gather All Symptoms Collect every observable fact before forming any theory. 1. Parse `$ARGUMENTS` as the symptom description 2. Extract the available facts from `$ARGUMENTS` and note which are unknown — capture gaps rather than prompting interactively (see the fork note under "Tool Usage by Phase"): - Expected vs actual behavior - When it started / what changed recently - Consistent or intermittent - Error messages, logs, or stack traces If a gap blocks the investigation, exhaust the codebase, git history, and tests first; only then surface the specific questions in the final report (per the Phase 5 gate). 3. Check memory files for known pitfalls related to this area: - Read MEMORY.md and any topic-specific memory files - Check CLAUDE.md for documented patterns 4. Gather environmental context: - Run `git log --oneline -20` to see recent changes - Run `git diff --stat HEAD~5` to see what files changed recently - Check for any failing tests with the project's test runner **Output:** A symptom report listing every observable fact, recent changes, and any relevant memory entries. **Gate:** Do NOT theorize yet. Only facts. --- ### Phase 2: REPRODUCE — Confirm the Issue An issue you cannot reproduce is an issue you cannot prove you fixed. 1. Identify the shortest path to trigger the symptom: - Run existing tests that cover the affected area - If no test exists, attempt manual reproduction via Bash - For UI issues, use Playwright MCP for precise reproduction: 1. `playwright_navigate` to the affected page 2. `playwright_screenshot` to capture initial state 3. Replay the interaction sequence (`playwright_click`, `playwright_fill`, etc.) 4. `playwright_screenshot` to capture the error state 5. `playwright_console_logs` with `type: "error"` to capture JS errors 6. Use `start_codegen_session` to record the reproduction as a reusable test 2. Document the reproduction steps precisely 3. If the issue is **intermittent**: - Flag it as potentially timing-dependent (race condition, async, state) - Look for concurrent access, shared mutable state, missing locks/guards - Check for dependency on external state (network, filesystem, database) 4. If the issue **cannot be reproduced**: - Shift to forensic investigation (logs, git history, code review) - Do NOT skip remaining phases — proceed with available evidence **Output:** Reproduction steps, or explicit documentation of why reproduction failed. **Gate:** Issue confirmed (or forensic mode declared). Proceed. --- ### Phase 3: TRACE — Follow the Execution Path Start from the symptom and trace backward to the origin. 1. **Locate the symptom** — find the exact file and line where the error occurs: - Use Grep for error messages, exception types, log strings - Explore agent for broad searches if the location is unclear — unavailable when forked; batch parallel Grep/Glob calls inline instead 2. **Trace the call chain** — read every file in the execution path: - Use LSP `goToDefinition` and `findReferences` to navigate the call chain precisely - Use LSP `incomingCalls`/`outgoingCalls` to map the full call hierarchy - From error site → caller → caller's caller → entry point - Read each file fully with Read tool — do NOT skim - Document the complete flow: input → transform → output 3. **Trace the data flow** — follow the data that caused the error: - What value caused the crash? Where did it come from? - Trace the value backward: variable → assignment → source → input 4. **Map dependencies** — what else touches this code path: - Use LSP `findReferences` to find all callers of the failing function (more precise than Grep) - Fall back to Grep if LSP is unavailable for the file type - Check for shared state, singletons, global variables - Look for recent changes in dependencies with `git log --oneline -- ` 5. **Check git forensics** — when was the problem introduced: - `git log --oneline -- ` — who changed these files and when? - `git blame ` on the suspicious lines — what commit introduced them? - If a clear suspect commit is found, read its full diff **Output:** Complete execution trace with file paths and line numbers. Data flow map. Git timeline. **Gate:** The full code path from entry point to symptom is mapped and understood. --- ### Phase 4: HYPOTHESIZE — Deep Reasoning with 5 Whys **This phase MUST use the sequential-thinking MCP server** for structured multi-step reasoning. 1. Start the sequential-thinking chain with the symptom and all evidence from Phases 1-3 2. Apply the **5 Whys method** — for each answer, ask "but why does THAT happen?": ``` Symptom: App crashes when tapping a document Why 1: DocumentDetailView accesses a deleted NSManagedObject Why 2: The object was deleted from Core Data while the view held a reference Why 3: context.delete() was called from a background operation Why 4: The background sync didn't check if the view was still displaying the object Why 5: There's no soft-delete pattern — objects are hard-deleted immediately ROOT CAUSE: Missing soft-delete guard in the sync pipeline ``` 3. Generate **at least 2 competing hypotheses** — don't lock on the first theory: - Categorize each by type: Code Logic | Data State | Timing/Race | Environment | Dependency | Configuration - For each hypothesis, define what evidence would prove or disprove it 4. Use **branching** in sequential-thinking to explore alternative explanations: ``` branchFromThought: 3, branchId: "alternative-cause" ``` 5. Rank hypotheses by likelihood based on available evidence **Output:** Ranked list of hypotheses with evidence requirements for each. **Gate:** At least 2 hypotheses generated. Each has defined proof criteria. --- ### Phase 5: PROVE — Test Each Hypothesis with Evidence Systematically confirm or eliminate each hypothesis. No guessing. **For each hypothesis (highest-ranked first):** 1. **Gather confirming evidence:** - Read the specific code paths predicted by the hypothesis - Check logs/output for patterns the hypothesis predicts - Run targeted tests that would pass if the hypothesis is correct - Use `git blame` / `git log` to check if timing matches 2. **Gather disconfirming evidence:** - Look for code paths that should also fail if the hypothesis is correct but don't - Check edge cases that contradict the hypothesis 3. **Check external sources:** - Use WebSearch for known issues in the library/framework version - Use library-docs skill (context7 MCP) to verify correct API usage - Search GitHub issues for the library: `mcp__github__search_issues` 4. **Verdict per hypothesis:** - **CONFIRMED** — evidence supports it, no contradictions - **ELIMINATED** — evidence contradicts it - **INCONCLUSIVE** — need more evidence (define what) **If all hypotheses are eliminated:** Return to Phase 4 with new evidence. Generate new hypotheses. **Output:** Evidence log per hypothesis. One confirmed root cause (or request for more data). **Gate:** Exactly one root cause confirmed with evidence. Or an explicit statement that the cause requires additional data from the user (with specific questions). --- ### Phase 6: ROOT CAUSE — Document the Causal Chain Write the definitive explanation before touching any code. 1. Document the complete causal chain: ``` ROOT CAUSE: → causes: → causes: → manifests as: ``` 2. Explain **why** this is the root cause (not just a proximate cause): - If fixed, would it prevent recurrence? (yes = root cause) - Is there a deeper cause? (if yes, keep digging) 3. Identify the **blast radius** — what else is affected: - Are there similar patterns elsewhere in the codebase? - Use Grep to find analogous code that may have the same bug 4. Present the root cause analysis for approval before proceeding to fix **Output:** Root cause statement, causal chain, blast radius assessment. **Gate — HARD HALT. Consent is required, and silence is never consent.** Phase 7 may begin only after the user has seen this diagnosis and approved a fix. - **Forked run (`context: fork` — the default): STOP HERE.** End the run at Phase 6, return the root-cause report as the final answer, and do NOT enter Phase 7 or Phase 8. Consent cannot be obtained mid-run because a forked run cannot use AskUserQuestion, so the fix is out of scope for this invocation by construction. Close the report with: "Root cause proven — approve to proceed with the fix (Phases 7-8)." - **Un-forked only:** present the diagnosis, obtain the user's explicit agreement, then continue to Phase 7. No agreement, no fix — stop here instead. - **Resuming:** Phases 7-8 run in a *subsequent* invocation that carries the user's approval of this diagnosis. The approval must be present in that invocation; never infer it from the fact that an investigation already ran. --- ### Phase 7: FIX — Address the Root Cause Fix the root cause, not the symptom. Minimal, targeted change. **Precondition — do not start without it:** the Phase 6 consent gate is satisfied, i.e. this invocation carries the user's approval of the diagnosis. A forked run has already ended at Phase 6 and never reaches this phase. If you cannot point to that approval, stop and return the Phase 6 report instead. 1. Design the fix: - What is the minimum change that eliminates the root cause? - Does the fix handle all cases in the blast radius (Phase 6)? - Does the fix introduce any new risks? 2. Implement the fix: - Read every file before modifying it - Make the smallest change possible - Add inline comments only where the fix is non-obvious 3. Verify the fix: - Run the reproduction steps from Phase 2 — symptom should be gone - Run existing tests — no regressions - Run code-quality agent on modified files if the change is substantial 4. Check for similar patterns: - If the bug was a pattern (e.g., missing null check), search for the same pattern elsewhere - Fix all instances, not just the reported one **Output:** Code changes with explanation of what was changed and why. --- ### Phase 8: PREVENT — Ensure It Never Recurs The investigation isn't complete until recurrence is prevented. 1. **Add a regression test** that would have caught this bug: - The test must fail without the fix and pass with it - Use test-automation agent for comprehensive test generation 2. **Update project memory** if a new pitfall was discovered: - Add to MEMORY.md under Common Pitfalls - Include the pattern, why it's dangerous, and the safe alternative 3. **Suggest structural improvements** (optional, only if the bug reveals a design flaw): - Propose architectural changes that make this class of bug impossible - Present as a suggestion, not an immediate action 4. **Write the investigation summary:** ``` ## Investigation Report **Symptom:** **Root Cause:** **Causal Chain:** root cause → ... → symptom **Fix:** **Blast Radius:** **Regression Test:** **Prevention:** **Time:** ``` --- ## Tool Usage by Phase | Phase | Primary Tools | When to Use Agents | |-------|--------------|-------------------| | 1. OBSERVE | Read, Grep, Bash (git log) | — | | 2. REPRODUCE | Bash (test runner), Playwright MCP | — | | 3. TRACE | Read, Grep, Glob, Bash (git blame) | Explore agent for broad searches (un-forked only) | | 4. HYPOTHESIZE | sequential-thinking MCP | deep-analysis skill | | 5. PROVE | Read, Grep, Bash, WebSearch, context7 MCP | library-docs skill, GitHub MCP | | 6. ROOT CAUSE | Read, Grep | Explore agent for blast radius (un-forked only) | | 7. FIX | Read, Edit, Write, Bash | code-quality agent for review | | 8. PREVENT | Write, Edit, Bash | test-automation agent for tests | > **Fork note:** `/investigate` runs forked (`context: fork`) for context isolation — the deep trace/evidence stays out of the main conversation and only the root-cause report returns. Forked subagents cannot use the `Agent` launcher or `AskUserQuestion`, so the "When to Use Agents" column (Explore / code-quality / test-automation) and any user clarification apply only when this protocol is run un-forked. When forked (the default), perform those steps inline with the Primary Tools and surface any needed user input in the final report. Because consent cannot be collected mid-run, **Phase 6 is a hard halt when forked** — the run ends with the root-cause report, and Phases 7-8 wait for a subsequent, approval-carrying invocation (see the Phase 6 gate, which is authoritative). (Core RCA runs on Primary Tools — Read/Grep/Bash/sequential-thinking/Playwright/context7/GitHub/LSP — all available to subagents, so fork costs nothing for the core.) ## Anti-Patterns — What This Skill Prevents | Bad Habit | What `/investigate` Does Instead | |-----------|--------------------------------| | Jump straight to fixing | Forces Phases 1-6 before any code change | | Fix the symptom | 5 Whys drills to root cause | | Single theory tunnel vision | Requires 2+ competing hypotheses | | "It works now" without understanding | Demands evidence-based proof | | Fix one instance, miss others | Blast radius analysis in Phase 6 | | No regression test | Phase 8 mandates a test | | Knowledge lost | Memory update in Phase 8 | ## When to Use `/investigate` vs Other Tools | Situation | Use | |-----------|-----| | Bug, crash, error, unexpected behavior | `/investigate` | | **Live production outage** — service down, users impacted, active incident | **incident-commander FIRST** — mitigate and restore, then `/investigate` for the RCA | | Build a new feature | `/execute` | | Quick "what does this code do?" | Explore agent directly (main session only) | | Performance slow but unclear why | `/investigate` (treat slowness as symptom) | | Known fix, just need to apply it | Direct Edit — no investigation needed | | Security vulnerability found | `/investigate` + security-scan | ## References See [references/investigation-frameworks.md](references/investigation-frameworks.md) for detailed methodology guides.