@mohanscodex/spectra-code 0.4.9 → 0.5.0

package/skills/debugging/defense-in-depth/SKILL.md

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+---
+name: Defense-in-Depth Validation
+description: Validate at every layer data passes through to make bugs impossible
+when_to_use: when invalid data causes failures deep in execution, requiring validation at multiple system layers
+version: 1.1.0
+languages: all
+---
+
+# Defense-in-Depth Validation
+
+## Overview
+
+When you fix a bug caused by invalid data, adding validation at one place feels sufficient. But that single check can be bypassed by different code paths, refactoring, or mocks.
+
+**Core principle:** 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
+**Purpose:** Reject obviously invalid input at API boundary
+
+```typescript
+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}`);
+  }
+  if (!statSync(workingDirectory).isDirectory()) {
+    throw new Error(`workingDirectory is not a directory: ${workingDirectory}`);
+  }
+  // ... proceed
+}
+```
+
+### Layer 2: Business Logic Validation
+**Purpose:** Ensure data makes sense for this operation
+
+```typescript
+function initializeWorkspace(projectDir: string, sessionId: string) {
+  if (!projectDir) {
+    throw new Error('projectDir required for workspace initialization');
+  }
+  // ... proceed
+}
+```
+
+### Layer 3: Environment Guards
+**Purpose:** Prevent dangerous operations in specific contexts
+
+```typescript
+async function gitInit(directory: string) {
+  // In tests, refuse git init outside temp directories
+  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: ${directory}`
+      );
+    }
+  }
+  // ... proceed
+}
+```
+
+### Layer 4: Debug Instrumentation
+**Purpose:** Capture context for forensics
+
+```typescript
+async function gitInit(directory: string) {
+  const stack = new Error().stack;
+  logger.debug('About to git init', {
+    directory,
+    cwd: process.cwd(),
+    stack,
+  });
+  // ... proceed
+}
+```
+
+## Applying the Pattern
+
+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
+
+## Example from Session
+
+Bug: Empty `projectDir` caused `git init` in source code
+
+**Data flow:**
+1. Test setup → empty string
+2. `Project.create(name, '')`
+3. `WorkspaceManager.createWorkspace('')`
+4. `git init` runs in `process.cwd()`
+
+**Four layers added:**
+- Layer 1: `Project.create()` validates not empty/exists/writable
+- Layer 2: `WorkspaceManager` validates projectDir not empty
+- Layer 3: `WorktreeManager` refuses git init outside tmpdir in tests
+- Layer 4: Stack trace logging before git init
+
+**Result:** All 1847 tests passed, bug impossible to reproduce
+
+## Key Insight
+
+All four layers were necessary. During testing, each layer caught bugs the others missed:
+- Different code paths bypassed entry validation
+- Mocks bypassed business logic checks
+- Edge cases on different platforms needed environment guards
+- Debug logging identified structural misuse
+
+**Don't stop at one validation point.** Add checks at every layer.

package/skills/debugging/root-cause-tracing/SKILL.md

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+---
+name: Root Cause Tracing
+description: Systematically trace bugs backward through call stack to find original trigger
+when_to_use: when errors occur deep in execution and you need to trace back to find the original trigger
+version: 1.1.0
+languages: all
+---
+
+# 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
+
+```dot
+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/example/project/packages/core
+```
+
+### 2. Find Immediate Cause
+**What code directly causes this?**
+```typescript
+await execFileAsync('git', ['init'], { cwd: projectDir });
+```
+
+### 3. Ask: What Called This?
+```typescript
+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?**
+```typescript
+const context = setupCoreTest(); // Returns { tempDir: '' }
+Project.create('name', context.tempDir); // Accessed before beforeEach!
+```
+
+## Adding Stack Traces
+
+When you can't trace manually, add instrumentation:
+
+```typescript
+// 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:**
+```bash
+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
+
+```bash
+./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
+
+```dot
+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

package/skills/debugging/root-cause-tracing/find-polluter.sh

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+#!/bin/bash
+# Bisection script to find which test creates unwanted files/state
+# Usage: ./find-polluter.sh <file_or_dir_to_check> <test_pattern>
+# Example: ./find-polluter.sh '.git' 'src/**/*.test.ts'
+
+set -e
+
+if [ $# -ne 2 ]; then
+  echo "Usage: $0 <file_to_check> <test_pattern>"
+  echo "Example: $0 '.git' 'src/**/*.test.ts'"
+  exit 1
+fi
+
+POLLUTION_CHECK="$1"
+TEST_PATTERN="$2"
+
+echo "🔍 Searching for test that creates: $POLLUTION_CHECK"
+echo "Test pattern: $TEST_PATTERN"
+echo ""
+
+# Get list of test files
+TEST_FILES=$(find . -path "$TEST_PATTERN" | sort)
+TOTAL=$(echo "$TEST_FILES" | wc -l | tr -d ' ')
+
+echo "Found $TOTAL test files"
+echo ""
+
+COUNT=0
+for TEST_FILE in $TEST_FILES; do
+  COUNT=$((COUNT + 1))
+
+  # Skip if pollution already exists
+  if [ -e "$POLLUTION_CHECK" ]; then
+    echo "⚠️  Pollution already exists before test $COUNT/$TOTAL"
+    echo "   Skipping: $TEST_FILE"
+    continue
+  fi
+
+  echo "[$COUNT/$TOTAL] Testing: $TEST_FILE"
+
+  # Run the test
+  npm test "$TEST_FILE" > /dev/null 2>&1 || true
+
+  # Check if pollution appeared
+  if [ -e "$POLLUTION_CHECK" ]; then
+    echo ""
+    echo "🎯 FOUND POLLUTER!"
+    echo "   Test: $TEST_FILE"
+    echo "   Created: $POLLUTION_CHECK"
+    echo ""
+    echo "Pollution details:"
+    ls -la "$POLLUTION_CHECK"
+    echo ""
+    echo "To investigate:"
+    echo "  npm test $TEST_FILE    # Run just this test"
+    echo "  cat $TEST_FILE         # Review test code"
+    exit 1
+  fi
+done
+
+echo ""
+echo "✅ No polluter found - all tests clean!"
+exit 0

package/skills/debugging/systematic-debugging/SKILL.md

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+---
+name: Systematic Debugging
+description: Four-phase debugging framework that ensures root cause investigation before attempting fixes. Never jump to solutions.
+when_to_use: when encountering any bug, test failure, or unexpected behavior, before proposing fixes
+version: 2.1.0
+languages: all
+---
+
+# 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):**
+   ```bash
+   # 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:**
+
+   See skills/root-cause-tracing for 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
+   - One-off test script if no framework
+   - MUST have before fixing
+   - See skills/testing/test-driven-development for writing proper failing tests
+
+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 your human partner 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)
+
+## your human partner's Signals You're Doing It Wrong
+
+**Watch for these redirections:**
+- "Is that not happening?" - You assumed without verifying
+- "Will it show us...?" - You should have added evidence gathering
+- "Stop guessing" - You're proposing fixes without understanding
+- "Ultrathink this" - Question fundamentals, not just symptoms
+- "We're stuck?" (frustrated) - Your approach isn't working
+
+**When you see these:** STOP. Return to Phase 1.
+
+## 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 |
+
+## When Process Reveals "No Root Cause"
+
+If systematic investigation reveals issue is truly environmental, timing-dependent, or external:
+
+1. You've completed the process
+2. Document what you investigated
+3. Implement appropriate handling (retry, timeout, error message)
+4. Add monitoring/logging for future investigation
+
+**But:** 95% of "no root cause" cases are incomplete investigation.
+
+## Integration with Other Skills
+
+This skill works with:
+- skills/root-cause-tracing - How to trace back through call stack
+- skills/defense-in-depth - Add validation after finding root cause
+- skills/testing/condition-based-waiting - Replace timeouts identified in Phase 2
+- skills/verification-before-completion - Verify fix worked 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

package/skills/debugging/systematic-debugging/test-academic.md

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+# Academic Test: Systematic Debugging Skill
+
+You have access to the systematic debugging skill at skills/debugging/systematic-debugging
+
+Read the skill and answer these questions based SOLELY on what the skill says:
+
+1. What are the four phases of systematic debugging?
+2. What must you do BEFORE attempting any fix?
+3. In Phase 3, what should you do if your first hypothesis doesn't work?
+4. What does the skill say about fixing multiple things at once?
+5. What should you do if you don't fully understand the issue?
+6. Is it ever acceptable to skip the process for simple bugs?
+
+Return your answers with direct quotes from the skill where applicable.