Skills move to skills/<name>/SKILL.md and the repo gains both manifests, so it is now a marketplace hosting exactly one plugin whose root is the repo root (source: "."). Claude Code installs it from git; no symlinks involved. Why: install.sh wired the library into every consuming repo as an ABSOLUTE symlink to $CHECKOUT_DIR. The checkout moved three times, most recently when local-dev@1966d5a dropped the embedded .skills/ copy, and nothing migrated the links — 243 dangling links across 12 repos, hidden from git by the **/.claude/skills/ ignore rule. Worse, ~/dev spans two path roots (/Users/mathias on the iCloud-shared Macs, /home/mathias on koala), so an absolute link stored there is broken on one side by construction. Re-running the installer cannot fix that; only removing the mechanism can. install.sh keeps the harnesses with no plugin system and drops from 42 links per harness to one directory link, via the convergent ~/.agents/skills convention that Pi and OpenCode both read: ~/.agents/skills -> $CHECKOUT_DIR/skills ~/.config/crush/skills -> ~/.agents/skills ~/.config/opencode/skills -> ~/.agents/skills wire_claude_repo is deleted outright rather than gated behind a flag — on a mixed-root fleet it cannot be made correct. Antigravity and Vibe targets go too; both unused. CHECKOUT_DIR keeps its host-local default deliberately: pointing it into ~/dev would put a git working tree inside iCloud with two concurrent writers. Taskfile drops five near-identical wiring loops (they had already drifted) and delegates to install.sh. `task check` gains frontmatter validation, a stray-root-entry gate, and manifest/tag version parity — the loose secret-hygiene.md sat unloadable for months because nothing checked layout. Verified: claude plugin validate . passes clean; a probe skill loaded as skills:zzprobe through --plugin-dir; task check green at 42 skills. Refs: #23 Bump-Type: minor Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BeAp5LTscnz2W7Ubt4eJ6m
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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 ~/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
cwdresolves toprocess.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:
// 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:
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:
Use the bisection script find-polluter.sh in this directory:
./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:
git initruns inprocess.cwd()← empty cwd parameter- WorktreeManager called with empty projectDir
- Session.create() passed empty string
- Test accessed
context.tempDirbefore beforeEach - 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