Index KnowledgeCAUTION

A SQL database in Rust: SQLite-compatible, now also speaking Postgres (experimental). The LLVM of databases.

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: index-knowledge
description: Generate hierarchical AGENTS.md knowledge base for a codebase. Creates root + complexity-scored subdirectory documentation.
---

# index-knowledge

Generate hierarchical AGENTS.md files. Root + complexity-scored subdirectories.

## Usage

```
--create-new   # Read existing → remove all → regenerate from scratch
--max-depth=2  # Limit directory depth (default: 5)
```

Default: Update mode (modify existing + create new where warranted)

---

## Workflow (High-Level)

1. **Discovery + Analysis** (concurrent)
   - Launch parallel explore agents (multiple Task calls in one message)
   - Main session: bash structure + LSP codemap + read existing AGENTS.md
2. **Score & Decide** - Determine AGENTS.md locations from merged findings
3. **Generate** - Root first, then subdirs in parallel
4. **Review** - Deduplicate, trim, validate

<critical>
**TodoWrite ALL phases. Mark in_progress → completed in real-time.**
  
```
TodoWrite([
  { id: "discovery", content: "Fire explore agents + LSP codemap + read existing", status: "pending", priority: "high" },
  { id: "scoring", content: "Score directories, determine locations", status: "pending", priority: "high" },
  { id: "generate", content: "Generate AGENTS.md files (root + subdirs)", status: "pending", priority: "high" },
  { id: "review", content: "Deduplicate, validate, trim", status: "pending", priority: "medium" }
])
```
</critical>

---

## Phase 1: Discovery + Analysis (Concurrent)

**Mark "discovery" as in_progress.**

### Launch Parallel Explore Agents

Multiple Task calls in a single message execute in parallel. Results return directly.

```
// All Task calls in ONE message = parallel execution

Task(
  description="project structure",
  subagent_type="explore",
  prompt="Project structure: PREDICT standard patterns for detected language → REPORT deviations only"
)

Task(
  description="entry points",
  subagent_type="explore",
  prompt="Entry points: FIND main files → REPORT non-standard organization"
)

Task(
  description="conventions",
  subagent_type="explore",
  prompt="Conventions: FIND config files (.eslintrc, pyproject.toml, .editorconfig) → REPORT project-specific rules"
)

Task(
  description="anti-patterns",
  subagent_type="explore",
  prompt="Anti-patterns: FIND 'DO NOT', 'NEVER', 'ALWAYS', 'DEPRECATED' comments → LIST forbidden patterns"
)

Task(
  description="build/ci",
  subagent_type="explore",
  prompt="Build/CI: FIND .github/workflows, Makefile → REPORT non-standard patterns"
)

Task(
  description="test patterns",
  subagent_type="explore",
  prompt="Test patterns: FIND test configs, test structure → REPORT unique conventions"
)
```

<dynamic-agents>
**DYNAMIC AGENT SPAWNING**: After bash analysis, spawn ADDITIONAL explore agents based on project scale:

| Factor | Threshold | Additional Agents |
|--------|-----------|-------------------|
| **Total files** | >100 | +1 per 100 files |
| **Total lines** | >10k | +1 per 10k lines |
| **Directory depth** | ≥4 | +2 for deep exploration |
| **Large files (>500 lines)** | >10 files | +1 for complexity hotspots |
| **Monorepo** | detected | +1 per package/workspace |
| **Multiple languages** | >1 | +1 per language |

```bash
# Measure project scale first
total_files=$(find . -type f -not -path '*/node_modules/*' -not -path '*/.git/*' | wc -l)
total_lines=$(find . -type f \( -name "*.ts" -o -name "*.py" -o -name "*.go" \) -not -path '*/node_modules/*' -exec wc -l {} + 2>/dev/null | tail -1 | awk '{print $1}')
large_files=$(find . -type f \( -name "*.ts" -o -name "*.py" \) -not -path '*/node_modules/*' -exec wc -l {} + 2>/dev/null | awk '$1 > 500 {count++} END {print count+0}')
max_depth=$(find . -type d -not -path '*/node_modules/*' -not -path '*/.git/*' | awk -F/ '{print NF}' | sort -rn | head -1)
```

Example spawning (all in ONE message for parallel execution):
```
// 500 files, 50k lines, depth 6, 15 large files → spawn additional agents
Task(
  description="large files",
  subagent_type="explore",
  prompt="Large file analysis: FIND files >500 lines, REPORT complexity hotspots"
)

Task(
  description="deep modules",
  subagent_type="explore",
  prompt="Deep modules at depth 4+: FIND hidden patterns, internal conventions"
)

Task(
  description="cross-cutting",
  subagent_type="explore",
  prompt="Cross-cutting concerns: FIND shared utilities across directories"
)
// ... more based on calculation
```
</dynamic-agents>

### Main Session: Concurrent Analysis

**While Task agents execute**, main session does:

#### 1. Bash Structural Analysis
```bash
# Directory depth + file counts
find . -type d -not -path '*/\.*' -not -path '*/node_modules/*' -not -path '*/venv/*' -not -path '*/dist/*' -not -path '*/build/*' | awk -F/ '{print NF-1}' | sort -n | uniq -c

# Files per directory (top 30)
find . -type f -not -path '*/\.*' -not -path '*/node_modules/*' | sed 's|/[^/]*$||' | sort | uniq -c | sort -rn | head -30

# Code concentration by extension
find . -type f \( -name "*.py" -o -name "*.ts" -o -name "*.tsx" -o -name "*.js" -o -name "*.go" -o -name "*.rs" \) -not -path '*/node_modules/*' | sed 's|/[^/]*$||' | sort | uniq -c | sort -rn | head -20

# Existing AGENTS.md / CLAUDE.md
find . -type f \( -name "AGENTS.md" -o -name "CLAUDE.md" \) -not -path '*/node_modules/*' 2>/dev/null
```

#### 2. Read Existing AGENTS.md
```
For each existing file found:
  Read(filePath=file)
  Extract: key insights, conventions, anti-patterns
  Store in EXISTING_AGENTS map
```

If `--create-new`: Read all existing first (preserve context) → then delete all → regenerate.

#### 3. LSP Codemap (if available)
```
lsp_servers()  # Check availability

# Entry points (parallel)
lsp_document_symbols(filePath="src/index.ts")
lsp_document_symbols(filePath="main.py")

# Key symbols (parallel)
lsp_workspace_symbols(filePath=".", query="class")
lsp_workspace_symbols(filePath=".", query="interface")
lsp_workspace_symbols(filePath=".", query="function")

# Centrality for top exports
l

CAUTIONgrade B · trust 89/100 Install with care. The audit found things worth knowing before you trust its output.

What the source does

Filesystem

none-observed

Network

none-observed

Shell

none-observed

Dependencies

pinned

Secrets in source

none-found

Findings (6)

.claude/skills/debugging/scripts

.codex/skills

If `--create-new`: Read all existing first (preserve context) → then delete all → regenerate.

.claude/skills/debugging/references/CORRUPTION-TOOLS.md

CLAUDE.md

examples/java/EncryptionExample.java

Gates applied: no_behavioural_pass.

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