TL;DR

4-phase process: Root Cause Investigation → Pattern Analysis → Hypothesis & Testing → Implementation. No fixes without root cause. 3+ failed fixes = question architecture. Use $root-cause or $trace to activate.

Systematic Debugging

Activation

1. Activate on $codex-systematic-debugging, $root-cause, or $trace.
2. Activate when encountering any bug, test failure, or unexpected behavior.
3. Activate when codex-workflow-autopilot routes to debug or fix workflow.
4. Activate when codex-intent-context-analyzer detects debug intent.
5. Activate when previous fix attempts failed.

Announce at start: "I'm using codex-systematic-debugging to investigate root cause."

The Iron Law

NO FIXES WITHOUT ROOT CAUSE INVESTIGATION FIRST

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

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.

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)
• Deadline is tight (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: Environment
   echo "=== ENV check ==="
   echo "DB_HOST: ${DB_HOST:+SET}${DB_HOST:-UNSET}"
   
   # Layer 2: Application config
   echo "=== Config loaded ==="
   node -e "console.log(require('./config').database)"
   
   # Layer 3: Connection
   echo "=== DB connection test ==="
   node -e "require('./db').ping().then(r => console.log(r))"
   
   # Layer 4: Query
   echo "=== Query test ==="
   node -e "require('./db').query('SELECT 1').then(r => console.log(r))"
   

   This reveals: Which layer fails (env → config ✓, config → connection ✗)

5. Trace Data Flow

   WHEN error is deep in call stack:

   See references/root-cause-tracing.md 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
   • Use codex-test-driven-development skill for writing proper failing tests
   • 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?
   • Run $gate or $check for full verification

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 (Phase 4.5 below)
   • DON'T attempt Fix #4 without architectural discussion

Phase 4.5: Question Architecture (3+ Failed Fixes)

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 human 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

Excuse	Reality
"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

Phase	Key Activities	Success Criteria
1. Root Cause	Read errors, reproduce, check changes, gather evidence	Understand WHAT and WHY
2. Pattern	Find working examples, compare	Identify differences
3. Hypothesis	Form theory, test minimally	Confirmed or new hypothesis
4. Implementation	Create test, fix, verify	Bug resolved, tests pass, gate green

CodexAI Integration

Gate Integration

After Phase 4 fix, verify through quality gate:

# Quick verification
python codex-execution-quality-gate/scripts/auto_gate.py --mode quick --project-root <repo>

# Smart test selection
python codex-execution-quality-gate/scripts/smart_test_selector.py --project-root <repo>

Workflow Integration

Alias	Behavior
$debug	Activates .workflows/debug.md + this skill
$root-cause	Jump directly to Phase 1
$trace	Jump to data flow tracing (Phase 1, Step 5)

Supporting Techniques

Available in references/ 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

Related Skills

• codex-test-driven-development — For creating failing test case (Phase 4, Step 1)
• codex-execution-quality-gate — Verify fix via $gate before claiming success

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