Root Cause Tracing

Overview

Bugs often manifest deep in the call stack (git init in wrong directory, file created in wrong location, database opened with wrong path). Your instinct is to fix where the error appears, but that's treating a symptom.

Core principle: Trace backward through the call chain until you find the original trigger, then fix at the source.

When to Use

digraph when_to_use {
    "Bug appears deep in stack?" [shape=diamond];
    "Can trace backwards?" [shape=diamond];
    "Fix at symptom point" [shape=box];
    "Trace to original trigger" [shape=box];
    "BETTER: Also add defense-in-depth" [shape=box];

    "Bug appears deep in stack?" -> "Can trace backwards?" [label="yes"];
    "Can trace backwards?" -> "Trace to original trigger" [label="yes"];
    "Can trace backwards?" -> "Fix at symptom point" [label="no - dead end"];
    "Trace to original trigger" -> "BETTER: Also add defense-in-depth";
}

Use when:

• Error happens deep in execution (not at entry point)
• Stack trace shows long call chain
• Unclear where invalid data originated
• Need to find which test/code triggers the problem

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?

Using Serena MCP for efficient call tracing:

• Use find_referencing_symbols(functionName) to get all callers with code context
• Returns symbolic information showing which functions/classes call your target
• Includes code snippets around each reference
• Much faster than manually searching

Example:

// Instead of manually searching, use Serena:
find_referencing_symbols("gitInit")
// Returns: WorktreeManager.createSessionWorktree() calls gitInit()
find_referencing_symbols("createSessionWorktree")
// Returns: Session.initializeWorkspace() calls createSessionWorktree()
// Continue tracing upward...

Manual tracing (if Serena unavailable):

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()
• That's the source code directory!

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:

Using Serena MCP for surgical instrumentation:

• Use insert_before_symbol to add diagnostic logging at function entry
• No need to read entire file or guess indentation
• Keeps logging changes isolated and minimal

// Use insert_before_symbol("gitInit", '...code...') to add:
const stack = new Error().stack;
console.error('DEBUG git init:', {
  directory,
  cwd: process.cwd(),
  nodeEnv: process.env.NODE_ENV,
  stack,
});

Manual insertion (if Serena unavailable):

// Before the problematic operation
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 });
}

Critical: Use console.error() in tests (not logger - may not show)

Run and capture (via subagent):

# (subagent) npm test 2>&1 | grep 'DEBUG git init'

Analyze stack traces:

• Look for test file names
• Find the line number triggering the call
• Identify the pattern (same test? same parameter?)

Finding Which Test Causes Pollution

If something appears during tests but you don't know which test:

Ask a research subagent to use the bisection script: ~/.claude/skills/root-cause-tracing/find-polluter.sh (return a cited Context Package with the first polluter)

# (subagent) ./find-polluter.sh '.git' 'src/**/*.test.ts'

Runs tests one-by-one, stops at first polluter. See script for usage.

Real Example: Empty projectDir

Symptom: .git created in packages/core/ (source code)

Trace chain:

1. git init runs in process.cwd() ← empty cwd parameter
2. WorktreeManager called with empty projectDir
3. Session.create() passed empty string
4. Test accessed context.tempDir before beforeEach
5. setupCoreTest() returns { tempDir: '' } initially

Root cause: Top-level variable initialization accessing empty value

Fix: Made tempDir a getter that throws if accessed before beforeEach

Also added defense-in-depth:

• Layer 1: Project.create() validates directory
• Layer 2: WorkspaceManager validates not empty
• Layer 3: NODE_ENV guard refuses git init outside tmpdir
• Layer 4: Stack trace logging before git init

Key Principle

digraph principle {
    "Found immediate cause" [shape=ellipse];
    "Can trace one level up?" [shape=diamond];
    "Trace backwards" [shape=box];
    "Is this the source?" [shape=diamond];
    "Fix at source" [shape=box];
    "Add validation at each layer" [shape=box];
    "Bug impossible" [shape=doublecircle];
    "NEVER fix just the symptom" [shape=octagon, style=filled, fillcolor=red, fontcolor=white];

    "Found immediate cause" -> "Can trace one level up?";
    "Can trace one level up?" -> "Trace backwards" [label="yes"];
    "Can trace one level up?" -> "NEVER fix just the symptom" [label="no"];
    "Trace backwards" -> "Is this the source?";
    "Is this the source?" -> "Trace backwards" [label="no - keeps going"];
    "Is this the source?" -> "Fix at source" [label="yes"];
    "Fix at source" -> "Add validation at each layer";
    "Add validation at each layer" -> "Bug impossible";
}

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

Stack Trace Tips

In tests: Use console.error() not logger - logger may be suppressed Before operation: Log before the dangerous operation, not after it fails Include context: Directory, cwd, environment variables, timestamps Capture stack: new Error().stack shows complete call chain

Real-World Impact

From debugging session (2025-10-03):

• Found root cause through 5-level trace
• Fixed at source (getter validation)
• Added 4 layers of defense
• 1847 tests passed, zero pollution