Systematically trace bugs backward through call stack to find original trigger. Use when errors occur deep in execution and you need to trace back to find the original trigger.
npx skills add https://github.com/secondsky/claude-skills --skill root-cause-tracing
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.
Use when:
Error: git init failed in ~/project/packages/core
What code directly causes this?
await execFileAsync('git', ['init'], { cwd: projectDir });
WorktreeManager.createSessionWorktree(projectDir, sessionId)
→ called by Session.initializeWorkspace()
→ called by Session.create()
→ called by test at Project.create()
What value was passed?
projectDir = '' (empty string!)cwd resolves to process.cwd()Where did empty string come from?
const context = setupCoreTest(); // Returns { tempDir: '' }
Project.create('name', context.tempDir); // Accessed before beforeEach!
When you can't trace manually, add instrumentation:
// 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:
bun test 2>&1 | grep 'DEBUG git init'
Analyze stack traces:
If something appears during tests but you don't know which test:
Use the bisection script to run tests one-by-one:
# Example: find which test creates .git in wrong place
bun test --run --bail 2>&1 | tee test-output.log
Runs tests one-by-one, stops at first polluter.
Symptom: .git created in packages/core/ (source code)
Trace chain:
git init runs in process.cwd() ← empty cwd parametercontext.tempDir before beforeEach{ tempDir: '' } initiallyRoot cause: Top-level variable initialization accessing empty value
Fix: Made tempDir a getter that throws if accessed before beforeEach
Also added defense-in-depth:
NEVER fix just where the error appears. Trace back to find the original trigger.
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
From debugging session:
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.
Build and distribute Expo development clients locally or via TestFlight
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Take secondsky/root-cause-tracing from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.