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Systematic Debugging

Jesse Vincent (obra)CommunityCreated by Jesse Vincent (obra)

  • Skill
  • Guidelines
  • Software development
  • MIT
  • Low risk
  • Has scripts

From the author

Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes
— the description by Jesse Vincent (obra)

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

Systematic Debugging is a disciplined approach to troubleshooting that mandates identifying the root cause of an issue before attempting any code changes. It rejects the 'guess-and-check' method, providing a structured process that moves through investigation, pattern analysis, hypothesis testing, and implementation. By enforcing strict adherence to evidence-based problem solving, this skill helps developers avoid the common pitfalls of thrashing, masking symptoms, and introducing new bugs through unverified fixes.

What it does

  • Provides a four-phase workflow for investigating and resolving bugs.
  • Mandates root cause identification before any fix is applied.
  • Offers techniques for multi-component system diagnostics and data flow tracing.
  • Defines clear stop-conditions for when to question the underlying architecture.
  • Includes a reference table to counter common rationalizations for skipping process.
  • Integrates with supporting techniques for tracing and defensive programming.

When to use it

  • When encountering test failures, production bugs, or unexpected behavior.
  • When under time pressure where guessing seems tempting.
  • When previous attempts to fix an issue have failed.
  • When you do not fully understand the nature of the problem.
  • When an issue appears simple but persists despite quick fixes.

Advantages

  • Prevents the cycle of 'fix-break-fix' by ensuring the root cause is addressed.
  • Reduces total time spent on debugging by eliminating ineffective trial-and-error.
  • Provides a clear, repeatable process that works across different technical domains.
  • Helps identify when an issue is architectural rather than a simple coding error.
  • Encourages the creation of automated tests to verify fixes.

Usage examples

“I have a failing test in my CI pipeline, what should I do?”
The agent will guide you through the four phases: investigating the error logs, reproducing the failure, checking recent changes, and gathering evidence at component boundaries before proposing a fix.
“I've tried three different fixes for this bug and it still isn't working, help.”
The agent will trigger the architectural review process, forcing a stop to further fixes and initiating a discussion on whether the underlying pattern or architecture is fundamentally flawed.

Install

  1. Download the skill as a ZIP:

    https://autogineer.com/agent-skills/obra/systematic-debugging/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip systematic-debugging.zip -d .agents/skills

Documentation by Jesse Vincent (obra)

Systematic Debugging

Overview

Core principle: ALWAYS find root cause before attempting fixes. Symptom fixes are failure.

Violating the letter of this process is violating the spirit of debugging.

The Iron Law

NO FIXES WITHOUT ROOT CAUSE INVESTIGATION FIRST

If you haven't completed Phase 1, you cannot propose fixes.

When to Use

Use for ANY technical issue:

  • Test failures

  • Bugs in production

  • Unexpected behavior

  • Performance problems

  • Build failures

  • Integration issues

Use this ESPECIALLY when:

  • Under time pressure (emergencies make guessing tempting)

  • "Just one quick fix" seems obvious

  • You've already tried multiple fixes

  • Previous fix didn't work

  • You don't fully understand the issue

Don't skip when:

  • Issue seems simple (simple bugs have root causes too)

  • You're in a hurry (rushing guarantees rework)

  • Manager wants it fixed NOW (systematic is faster than thrashing)

The Four Phases

You MUST complete each phase before proceeding to the next.

Phase 1: Root Cause Investigation

BEFORE attempting ANY fix:

  1. Read Error Messages Carefully

    • Don't skip past errors or warnings

    • They often contain the exact solution

    • Read stack traces completely

    • Note line numbers, file paths, error codes

  2. Reproduce Consistently

    • Can you trigger it reliably?

    • What are the exact steps?

    • Does it happen every time?

    • If not reproducible → gather more data, don't guess

  3. Check Recent Changes

    • What changed that could cause this?

    • Git diff, recent commits

    • New dependencies, config changes

    • Environmental differences

  4. Gather Evidence in Multi-Component Systems

    WHEN system has multiple components (CI → build → signing, API → service → database):

    BEFORE proposing fixes, add diagnostic instrumentation:

    For EACH component boundary:
      - Log what data enters component
      - Log what data exits component
      - Verify environment/config propagation
      - Check state at each layer
    
    Run once to gather evidence showing WHERE it breaks
    THEN analyze evidence to identify failing component
    THEN investigate that specific component

    Example (multi-layer system):

    # Layer 1: Workflow
    echo "=== Secrets available in workflow: ==="
    echo "IDENTITY: $([ -n "${IDENTITY:-}" ] && echo SET || echo UNSET)"
    
    # Layer 2: Build script
    echo "=== Env vars in build script: ==="
    printenv IDENTITY >/dev/null 2>&1 && echo "IDENTITY in environment" || echo "IDENTITY not in environment"
    
    # Layer 3: Signing script
    echo "=== Keychain state: ==="
    security list-keychains
    security find-identity -v
    
    # Layer 4: Actual signing
    codesign --sign "$IDENTITY" --verbose=4 "$APP"

    This reveals: Which layer fails (secrets → workflow ✓, workflow → build ✗)

  5. Trace Data Flow

    WHEN error is deep in call stack:

    See root-cause-tracing.md in this directory for the complete backward tracing technique.

    Quick version:

    • Where does bad value originate?

    • What called this with bad value?

    • Keep tracing up until you find the source

    • Fix at source, not at symptom

Phase 2: Pattern Analysis

Find the pattern before fixing:

  1. Find Working Examples

    • Locate similar working code in same codebase

    • What works that's similar to what's broken?

  2. Compare Against References

    • If implementing pattern, read reference implementation COMPLETELY

    • Don't skim - read every line

    • Understand the pattern fully before applying

  3. Identify Differences

    • What's different between working and broken?

    • List every difference, however small

    • Don't assume "that can't matter"

  4. Understand Dependencies

    • What other components does this need?

    • What settings, config, environment?

    • What assumptions does it make?

Phase 3: Hypothesis and Testing

Scientific method:

  1. Form Single Hypothesis

    • State clearly: "I think X is the root cause because Y"

    • Write it down

    • Be specific, not vague

  2. Test Minimally

    • Make the SMALLEST possible change to test hypothesis

    • One variable at a time

    • Don't fix multiple things at once

  3. Verify Before Continuing

    • Did it work? Yes → Phase 4

    • Didn't work? Form NEW hypothesis

    • DON'T add more fixes on top

  4. When You Don't Know

    • Say "I don't understand X"

    • Don't pretend to know

    • Ask for help

    • Research more

Phase 4: Implementation

Fix the root cause, not the symptom:

  1. Create Failing Test Case

    • Simplest possible reproduction

    • Automated test if possible

    • One-off test script if no framework

    • MUST have before fixing

    • Use the superpowers:test-driven-development skill for writing proper failing tests

  2. Implement Single Fix

    • Address the root cause identified

    • ONE change at a time

    • No "while I'm here" improvements

    • No bundled refactoring

  3. Verify Fix

    • Test passes now?

    • No other tests broken?

    • Issue actually resolved?

    • Use the superpowers:verification-before-completion skill before claiming success

  4. If Fix Doesn't Work

    • STOP

    • Count: How many fixes have you tried?

    • If < 3: Return to Phase 1, re-analyze with new information

    • If ≥ 3: STOP and question the architecture (step 5 below)

    • DON'T attempt Fix #4 without architectural discussion

  5. If 3+ Fixes Failed: Question Architecture

    Pattern indicating architectural problem:

    • Each fix reveals new shared state/coupling/problem in different place

    • Fixes require "massive refactoring" to implement

    • Each fix creates new symptoms elsewhere

    STOP and question fundamentals:

    • Is this pattern fundamentally sound?

    • Are we "sticking with it through sheer inertia"?

    • Should we refactor architecture vs. continue fixing symptoms?

    Discuss with your human partner before attempting more fixes

    This is NOT a failed hypothesis - this is a wrong architecture.

Red Flags - STOP and Follow Process

If you catch yourself thinking:

  • "Quick fix for now, investigate later"

  • "Just try changing X and see if it works"

  • "Add multiple changes, run tests"

  • "Skip the test, I'll manually verify"

  • "It's probably X, let me fix that"

  • "I don't fully understand but this might work"

  • "Pattern says X but I'll adapt it differently"

  • "Here are the main problems: [lists fixes without investigation]"

  • Proposing solutions before tracing data flow

  • "One more fix attempt" (when already tried 2+)

  • Each fix reveals new problem in different place

ALL of these mean: STOP. Return to Phase 1.

If 3+ fixes failed: Question the architecture (see Phase 4.5)

your human partner's Signals You're Doing It Wrong

Watch for these redirections:

  • "Is that not happening?" - You assumed without verifying

  • "Will it show us...?" - You should have added evidence gathering

  • "Stop guessing" - You're proposing fixes without understanding

  • "Ultra-think this" - Question fundamentals, not just symptoms

  • "We're stuck?" (frustrated) - Your approach isn't working

When you see these: STOP. Return to Phase 1.

Common Rationalizations

ExcuseReality
"Issue is simple, don't need process"Simple issues have root causes too. Process is fast for simple bugs.
"Emergency, no time for process"Systematic debugging is FASTER than guess-and-check thrashing.
"Just try this first, then investigate"First fix sets the pattern. Do it right from the start.
"I'll write test after confirming fix works"Untested fixes don't stick. Test first proves it.
"Multiple fixes at once saves time"Can't isolate what worked. Causes new bugs.
"Reference too long, I'll adapt the pattern"Partial understanding guarantees bugs. Read it completely.
"I see the problem, let me fix it"Seeing symptoms ≠ understanding root cause.
"One more fix attempt" (after 2+ failures)3+ failures = architectural problem. Question pattern, don't fix again.

Quick Reference

PhaseKey ActivitiesSuccess Criteria
1. Root CauseRead errors, reproduce, check changes, gather evidenceUnderstand WHAT and WHY
2. PatternFind working examples, compareIdentify differences
3. HypothesisForm theory, test minimallyConfirmed or new hypothesis
4. ImplementationCreate test, fix, verifyBug resolved, tests pass

When Process Reveals "No Root Cause"

If systematic investigation reveals issue is truly environmental, timing-dependent, or external:

  1. You've completed the process

  2. Document what you investigated

  3. Implement appropriate handling (retry, timeout, error message)

  4. Add monitoring/logging for future investigation

But: 95% of "no root cause" cases are incomplete investigation.

Supporting Techniques

These techniques are part of systematic debugging and available in this directory:

  • root-cause-tracing.md - Trace bugs backward through call stack to find original trigger

  • defense-in-depth.md - Add validation at multiple layers after finding root cause

  • condition-based-waiting.md - Replace arbitrary timeouts with condition polling

Files

condition-based-waiting.md

Condition-Based Waiting

Overview

Flaky tests often guess at timing with arbitrary delays. This creates race conditions where tests pass on fast machines but fail under load or in CI.

Core principle: Wait for the actual condition you care about, not a guess about how long it takes.

When to Use

digraph when_to_use {
    "Test uses setTimeout/sleep?" [shape=diamond];
    "Testing timing behavior?" [shape=diamond];
    "Document WHY timeout needed" [shape=box];
    "Use condition-based waiting" [shape=box];

    "Test uses setTimeout/sleep?" -> "Testing timing behavior?" [label="yes"];
    "Testing timing behavior?" -> "Document WHY timeout needed" [label="yes"];
    "Testing timing behavior?" -> "Use condition-based waiting" [label="no"];
}

Use when:

  • Tests have arbitrary delays (setTimeout, sleep, time.sleep())

  • Tests are flaky (pass sometimes, fail under load)

  • Tests timeout when run in parallel

  • Waiting for async operations to complete

Don't use when:

  • Testing actual timing behavior (debounce, throttle intervals)

  • Always document WHY if using arbitrary timeout

Core Pattern

// ❌ BEFORE: Guessing at timing
await new Promise(r => setTimeout(r, 50));
const result = getResult();
expect(result).toBeDefined();

// ✅ AFTER: Waiting for condition
await waitFor(() => getResult() !== undefined);
const result = getResult();
expect(result).toBeDefined();

Quick Patterns

ScenarioPattern
Wait for eventwaitFor(() => events.find(e => e.type === 'DONE'))
Wait for statewaitFor(() => machine.state === 'ready')
Wait for countwaitFor(() => items.length >= 5)
Wait for filewaitFor(() => fs.existsSync(path))
Complex conditionwaitFor(() => obj.ready && obj.value > 10)

Implementation

Generic polling function:

async function waitFor<T>(
  condition: () => T | undefined | null | false,
  description: string,
  timeoutMs = 5000
): Promise<T> {
  const startTime = Date.now();

  while (true) {
    const result = condition();
    if (result) return result;

    if (Date.now() - startTime > timeoutMs) {
      throw new Error(`Timeout waiting for ${description} after ${timeoutMs}ms`);
    }

    await new Promise(r => setTimeout(r, 10)); // Poll every 10ms
  }
}

See condition-based-waiting-example.ts in this directory for complete implementation with domain-specific helpers (waitForEvent, waitForEventCount, waitForEventMatch) from actual debugging session.

Common Mistakes

❌ Polling too fast: setTimeout(check, 1) - wastes CPU ✅ Fix: Poll every 10ms

❌ No timeout: Loop forever if condition never met ✅ Fix: Always include timeout with clear error

❌ Stale data: Cache state before loop ✅ Fix: Call getter inside loop for fresh data

When Arbitrary Timeout IS Correct

// Tool ticks every 100ms - need 2 ticks to verify partial output
await waitForEvent(manager, 'TOOL_STARTED'); // First: wait for condition
await new Promise(r => setTimeout(r, 200));   // Then: wait for timed behavior
// 200ms = 2 ticks at 100ms intervals - documented and justified

Requirements:

  1. First wait for triggering condition

  2. Based on known timing (not guessing)

  3. Comment explaining WHY

Real-World Impact

From debugging session (2025-10-03):

  • Fixed 15 flaky tests across 3 files

  • Pass rate: 60% → 100%

  • Execution time: 40% faster

  • No more race conditions

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs Node.js

Security

What our scanner noticed· Low risk

  • Scripts that your agent may run

This skill includes scripts that your agent may run. Read them before you use it.

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Attribution and licence

Created by
Jesse Vincent (obra)
Publisher
Jesse Vincent (obra) (Community)
Source
obra/superpowers · skills/systematic-debugging · commit 22f0b46
Licence
MIT License (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE)
  • ATTRIBUTION.md (written by AutoGineer)
Synced

AutoGineer is not affiliated with or endorsed by Jesse Vincent (obra) or Jesse Vincent (obra).

Download ZIP

The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download systematic-debugging.zip