Systematic Debugging

Overview

Random fixes waste time and create new bugs. Quick patches mask underlying issues.

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: ${IDENTITY:+SET}${IDENTITY:-UNSET}"
   
   # Layer 2: Build script
   echo "=== Env vars in build script: ==="
   env | grep IDENTITY || 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:

   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

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?

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 the user 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)

Common Rationalizations

Quick Reference

Technique: Root Cause Tracing

When bugs manifest deep in the call stack, trace backward to find the original trigger.

The Tracing Process

1. Observe the Symptom

   Error: git init failed in /Users/jesse/project/packages/core
   

2. Find Immediate Cause – What code directly causes this?

   await execFileAsync('git', ['init'], { cwd: projectDir })
   

3. Ask: What Called This?

   WorktreeManager.createSessionWorktree(projectDir, sessionId)
     → called by Session.initializeWorkspace()
     → called by Session.create()
     → called by test at Project.create()
   

4. Keep Tracing Up – What value was passed?

   • projectDir = '' (empty string!)
   • Empty string as cwd resolves to process.cwd()

5. Find Original Trigger – Where did empty string come from?

   const context = setupCoreTest() // Returns { tempDir: '' }
   Project.create('name', context.tempDir) // Accessed before beforeEach!
   

Adding Stack Traces

When you can’t trace manually, add instrumentation:

async function gitInit(directory: string) {
  const stack = new Error().stack
  console.error('DEBUG git init:', {
    directory,
    cwd: process.cwd(),
    nodeEnv: process.env.NODE_ENV,
    stack,
  })
  await execFileAsync('git', ['init'], { cwd: directory })
}

Tips:

• Use console.error() in tests (logger may be suppressed)
• Log before the dangerous operation, not after it fails
• Include context: directory, cwd, environment variables
• new Error().stack shows complete call chain

Finding Which Test Causes Pollution

If something appears during tests but you don’t know which test, use bisection:

# Run tests one-by-one, stop at first polluter
for f in src/**/*.test.ts; do
  npm test "$f" && [ -d .git ] && echo "POLLUTER: $f" && break
done

NEVER fix just where the error appears. Trace back to find the original trigger.

Technique: Defense-in-Depth Validation

After finding root cause, validate at EVERY layer data passes through. Make the bug structurally impossible.

Why Multiple Layers

• Single validation: “We fixed the bug”
• Multiple layers: “We made the bug impossible”

Different layers catch different cases:

• Entry validation catches most bugs
• Business logic catches edge cases
• Environment guards prevent context-specific dangers
• Debug logging helps when other layers fail

The Four Layers

Layer 1: Entry Point Validation – Reject invalid input at API boundary

function createProject(name: string, workingDirectory: string) {
  if (!workingDirectory || workingDirectory.trim() === '') {
    throw new Error('workingDirectory cannot be empty')
  }
  if (!existsSync(workingDirectory)) {
    throw new Error(`workingDirectory does not exist: ${workingDirectory}`)
  }
}

Layer 2: Business Logic Validation – Ensure data makes sense for operation

function initializeWorkspace(projectDir: string, sessionId: string) {
  if (!projectDir) {
    throw new Error('projectDir required for workspace initialization')
  }
}

Layer 3: Environment Guards – Prevent dangerous operations in specific contexts

async function gitInit(directory: string) {
  if (process.env.NODE_ENV === 'test') {
    const normalized = normalize(resolve(directory))
    const tmpDir = normalize(resolve(tmpdir()))
    if (!normalized.startsWith(tmpDir)) {
      throw new Error(`Refusing git init outside temp dir during tests`)
    }
  }
}

Layer 4: Debug Instrumentation – Capture context for forensics

async function gitInit(directory: string) {
  logger.debug('About to git init', {
    directory,
    cwd: process.cwd(),
    stack: new Error().stack,
  })
}

Applying Defense-in-Depth

When you find a bug:

1. Trace the data flow – Where does bad value originate? Where used?
2. Map all checkpoints – List every point data passes through
3. Add validation at each layer – Entry, business, environment, debug
4. Test each layer – Try to bypass layer 1, verify layer 2 catches it

Don’t stop at one validation point. Add checks at every layer.

Real-World Impact

From debugging sessions:

• Systematic approach: 15-30 minutes to fix
• Random fixes approach: 2-3 hours of thrashing
• First-time fix rate: 95% vs 40%
• New bugs introduced: Near zero vs common