Cornelius Self-Diagnostic

Run comprehensive diagnostics to verify all agent components are functioning correctly.

Quick Start

Run full diagnostics:

/self-diagnostic

Run specific test category:

/self-diagnostic commands-only
/self-diagnostic skills-only
/self-diagnostic agents-only
/self-diagnostic dependencies-only

State Dependencies

Arguments

$ARGUMENTS

Safety Principles

CRITICAL: These diagnostics are READ-ONLY and NEVER modify production data.

• All tests use read-only operations (search, grep, read)
• NO file creation in Brain/ directory during tests
• NO API calls to paid services (HeyGen, Gemini, etc.)
• Test outputs go to /tmp/cornelius-diagnostic/ only
• NO changelog creation during diagnostics

Diagnostic Categories

1. Infrastructure Tests

Verify core infrastructure is accessible:

# Test 1.1: Check vault path exists
test -d "Brain" && echo "PASS: Vault path exists" || echo "FAIL: Vault path missing"

# Test 1.2: Check permanent notes directory
test -d "Brain/02-Permanent" && echo "PASS: Permanent notes directory exists" || echo "FAIL: Permanent notes directory missing"

# Test 1.3: Check Local Brain Search is available
test -f "resources/local-brain-search/run_search.sh" && echo "PASS: Local Brain Search scripts exist" || echo "FAIL: Local Brain Search scripts missing"

# Test 1.4: Check Article Index exists
test -f "Brain/04-Output/Articles/ARTICLE-INDEX.md" && echo "PASS: Article Index exists" || echo "FAIL: Article Index missing"

2. Dependency Tests

Verify external dependencies are installed:

# Test 2.1: Python available
python3 --version 2>/dev/null && echo "PASS: Python3 available" || echo "FAIL: Python3 not found"

# Test 2.2: uv package manager (for epub-chapter-extractor)
uv --version 2>/dev/null && echo "PASS: uv available" || echo "FAIL: uv not found"

# Test 2.3: Check Local Brain Search can run (simple test)
cd resources/local-brain-search && python3 -c "import sqlite3; import json; print('PASS: Core Python modules available')" 2>/dev/null || echo "FAIL: Python modules missing"

# Test 2.4: Check mermaid-diagram MCP is responsive
# (Just verify the skill file exists - actual MCP test would require invocation)
test -f ".claude/agents/diagram-generator.md" && echo "PASS: Diagram generator agent configured" || echo "FAIL: Diagram generator agent missing"

3. Skills Validation Tests

Verify skills are properly configured (metadata valid):

# Test 3.1: List all skills and validate structure
for skill_dir in .claude/skills/*/; do
  skill_name=$(basename "$skill_dir")
  if [ -f "${skill_dir}SKILL.md" ]; then
    # Check for required frontmatter
    if head -1 "${skill_dir}SKILL.md" | grep -q "^---"; then
      if grep -q "^name:" "${skill_dir}SKILL.md" && grep -q "^description:" "${skill_dir}SKILL.md"; then
        echo "PASS: Skill '$skill_name' - valid metadata"
      else
        echo "FAIL: Skill '$skill_name' - missing name or description"
      fi
    else
      echo "FAIL: Skill '$skill_name' - missing frontmatter"
    fi
  else
    echo "FAIL: Skill '$skill_name' - missing SKILL.md"
  fi
done

4. Commands Validation Tests

Verify commands are properly configured:

# Test 4.1: List all commands and validate structure
for cmd_file in .claude/commands/*.md; do
  cmd_name=$(basename "$cmd_file" .md)
  if head -1 "$cmd_file" | grep -q "^---"; then
    if grep -q "^description:" "$cmd_file"; then
      echo "PASS: Command '/$cmd_name' - valid metadata"
    else
      echo "FAIL: Command '/$cmd_name' - missing description"
    fi
  else
    echo "FAIL: Command '/$cmd_name' - missing frontmatter"
  fi
done

5. Agents Validation Tests

Verify sub-agents are properly configured:

# Test 5.1: List all agents and validate structure
for agent_file in .claude/agents/*.md; do
  agent_name=$(basename "$agent_file" .md)
  if head -1 "$agent_file" | grep -q "^---"; then
    if grep -q "^name:" "$agent_file" || grep -q "^description:" "$agent_file"; then
      echo "PASS: Agent '$agent_name' - valid metadata"
    else
      echo "FAIL: Agent '$agent_name' - missing name or description"
    fi
  else
    echo "FAIL: Agent '$agent_name' - missing frontmatter"
  fi
done

Functional Tests (Safe Invocations)

These tests invoke actual skills/commands with READ-ONLY operations.

Test: /search-vault Command

This tests the semantic search and grep functionality:

Invoke /search-vault with query: "dopamine"
Expected: Returns at least 1 result from permanent notes

Run this test: Use the Skill tool to invoke search-vault with args "dopamine"

Success criteria:

• Command executes without error
• Returns at least 1 search result
• Does NOT create any files

Test: /recall Command

Tests 3-layer semantic search:

Invoke /recall with query: "decision making"
Expected: Returns layered results with connections

Run this test: Use the Skill tool to invoke recall with args "decision making"

Success criteria:

• Command executes without error
• Returns Layer 1, Layer 2, and Layer 3 results
• Does NOT create any files

Test: /find-connections Command

Tests connection discovery:

Invoke /find-connections with query: "Dopamine"
Expected: Returns connections for the Dopamine note

Run this test: Use the Skill tool to invoke find-connections with args "Dopamine"

Success criteria:

• Command executes without error
• Returns explicit and semantic connections
• Does NOT create any files

Test: /get-perspective-on Command

Tests perspective extraction:

Invoke /get-perspective-on with query: "AI agents"
Expected: Returns the user's perspective with note citations

Run this test: Use the Skill tool to invoke get-perspective-on with args "AI agents"

Success criteria:

• Command executes without error
• Returns perspective text with [[note citations]]
• Does NOT create any files

Test: Local Brain Search Direct

Tests local brain search scripts directly:

# Run semantic search
resources/local-brain-search/run_search.sh "consciousness" --limit 3 --json

# Run connections query
resources/local-brain-search/run_connections.sh --stats --json

# Run hub discovery
resources/local-brain-search/run_connections.sh --hubs --limit 5 --json

Success criteria:

• All three commands return valid JSON
• Search returns results with similarity scores
• Stats returns note count and connection count

Skipped Tests (Would Modify Data or Cost Money)

These tests are INTENTIONALLY SKIPPED to avoid side effects:

Diagnostic Execution Instructions

Full Diagnostic Run

1. Run infrastructure tests (bash commands above)
2. Run dependency tests (bash commands above)
3. Run skill validation tests (bash commands above)
4. Run command validation tests (bash commands above)
5. Run agent validation tests (bash commands above)
6. Run functional tests (invoke skills via Skill tool)
7. Compile results into summary report

Output Format

Present results as:

# Cornelius Self-Diagnostic Report
**Run Date:** [current date/time]
**Agent Version:** 01.25

## Summary
| Category | Passed | Failed | Skipped |
|----------|--------|--------|---------|
| Infrastructure | X | X | 0 |
| Dependencies | X | X | 0 |
| Skills | X | X | 0 |
| Commands | X | X | 0 |
| Agents | X | X | 0 |
| Functional Tests | X | X | X |

## Detailed Results

### Infrastructure Tests
[Results...]

### Dependency Tests
[Results...]

### Skills Validation
[Results...]

### Commands Validation
[Results...]

### Agents Validation
[Results...]

### Functional Tests
[Results...]

### Skipped Tests
[List with reasons...]

## Recommendations
[Any issues found and suggested fixes]

Argument Handling

Based on $ARGUMENTS:

• No arguments or "full": Run all safe tests
• "commands-only": Only test commands validation + functional
• "skills-only": Only test skills validation
• "agents-only": Only test agents validation
• "dependencies-only": Only test infrastructure + dependencies
• "quick": Only run validation tests (no functional invocations)

Notes

• This diagnostic is designed to be safe and repeatable
• Run after any configuration changes to verify agent health
• If functional tests fail, check the underlying dependency first
• Diagnostic output can be saved to /tmp/cornelius-diagnostic/ for review

Completion Checklist

• Infrastructure tests executed (vault path, permanent notes, Local Brain Search, Article Index)
• Dependency tests executed (Python3, uv, core modules, diagram agent)
• Skills validation completed (frontmatter, name, description for all skills)
• Commands validation completed (frontmatter, description for all commands)
• Agents validation completed (frontmatter, name/description for all agents)
• Functional tests executed (search-vault, recall, find-connections, get-perspective-on, Local Brain Search)
• Summary report generated with pass/fail/skip counts
• Recommendations provided for any failures