---
name: init-deep
description: "(builtin) Initialize hierarchical AGENTS.md knowledge base"
---
## Codex Harness Tool Compatibility

This skill may include examples copied from the OpenCode harness. In Codex, do not call OpenCode-only tools such as `call_omo_agent(...)`, `task(...)`, `background_output(...)`, or `team_*(...)` literally. Translate those examples to Codex native tools:

| OpenCode example | Codex tool to use |
| --- | --- |
| `call_omo_agent(subagent_type="explore", ...)` | `multi_agent_v1.spawn_agent({"message":"TASK: act as an explorer. ...","agent_type":"explorer","fork_context":false})` |
| `call_omo_agent(subagent_type="librarian", ...)` | `multi_agent_v1.spawn_agent({"message":"TASK: act as a librarian. ...","agent_type":"librarian","fork_context":false})` |
| `task(subagent_type="plan", ...)` | `multi_agent_v1.spawn_agent({"message":"TASK: act as a planning agent. ...","agent_type":"plan","fork_context":false})` |
| `task(subagent_type="oracle", ...)` for final verification | `multi_agent_v1.spawn_agent({"message":"TASK: act as a rigorous reviewer. ...","agent_type":"lazycodex-gate-reviewer","fork_context":false})` |
| `task(category="...", ...)` for implementation or QA | `multi_agent_v1.spawn_agent({"message":"TASK: act as an implementation or QA worker. ...","fork_context":false})` |
| `background_output(task_id="...")` | `multi_agent_v1.wait_agent(...)` for mailbox signals |
| `team_*(...)` | Use Codex native subagents via `multi_agent_v1.spawn_agent`, `multi_agent_v1.send_input`, `multi_agent_v1.wait_agent`, and `multi_agent_v1.close_agent` |

Role-specific behavior must be described in a self-contained `message`. Use `fork_context: false` to start the child with only the initial prompt (no parent history); use `fork_context: true` only when full parent history is truly required. Include any required conversation context, files, diffs, constraints, and requested skill names directly in the spawned agent's `message`. OMO installs these selectable agent roles into `~/.codex/agents/`: `explorer`, `librarian`, `plan`, `momus`, `metis`, `lazycodex-code-reviewer`, `lazycodex-qa-executor`, and `lazycodex-gate-reviewer` - pass the matching name as `agent_type` so the child gets that role's model and instructions. If the spawn tool exposes no `agent_type` parameter, omit it and describe the role inside `message`. If a code block below conflicts with this section, this section wins.

For work likely to exceed one wait cycle, require the child to send `WORKING: <task> - <current phase>` before long passes and `BLOCKED: <reason>` only when progress stops. A `multi_agent_v1.wait_agent` timeout only means no new mailbox update arrived. Treat a running child as alive. Fallback only when the child is completed without the deliverable, ack-only after followup, explicitly `BLOCKED:`, or no longer running.

# /init-deep

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

## Usage

```
/init-deep                      # Update mode: modify existing + create new where warranted
/init-deep --create-new         # Read existing → remove all → regenerate from scratch
/init-deep --max-depth=2        # Limit directory depth (default: 3)
```

---

## Workflow (High-Level)

1. **Discovery + Analysis** (concurrent)
   - Fire background explore agents immediately
   - 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.**

### Fire Background Explore Agents IMMEDIATELY

Don't wait-these run async while main session works.

```
// Fire all at once, collect results later
task(subagent_type="explore", load_skills=[], description="Explore project structure", run_in_background=true, prompt="Project structure: PREDICT standard patterns for detected language → REPORT deviations only")
task(subagent_type="explore", load_skills=[], description="Find entry points", run_in_background=true, prompt="Entry points: FIND main files → REPORT non-standard organization")
task(subagent_type="explore", load_skills=[], description="Find conventions", run_in_background=true, prompt="Conventions: FIND config files (.eslintrc, pyproject.toml, .editorconfig) → REPORT project-specific rules")
task(subagent_type="explore", load_skills=[], description="Find anti-patterns", run_in_background=true, prompt="Anti-patterns: FIND 'DO NOT', 'NEVER', 'ALWAYS', 'DEPRECATED' comments → LIST forbidden patterns")
task(subagent_type="explore", load_skills=[], description="Explore build/CI", run_in_background=true, prompt="Build/CI: FIND .github/workflows, Makefile → REPORT non-standard patterns")
task(subagent_type="explore", load_skills=[], description="Find test patterns", run_in_background=true, 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:
```
// 500 files, 50k lines, depth 6, 15 large files → spawn 5+5+2+1 = 13 additional agents
task(subagent_type="explore", load_skills=[], description="Analyze large files", run_in_background=true, prompt="Large file analysis: FIND files >500 lines, REPORT complexity hotspots")
task(subagent_type="explore", load_skills=[], description="Explore deep modules", run_in_background=true, prompt="Deep modules at depth 4+: FIND hidden patterns, internal conventions")
task(subagent_type="explore", load_skills=[], description="Find shared utilities", run_in_background=true, prompt="Cross-cutting concerns: FIND shared utilities across directories")
// ... more based on calculation
```
</dynamic-agents>

### Main Session: Concurrent Analysis

**While background agents run**, 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)
```
LspServers()  # Check availability

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

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

# Centrality for top exports
LspFindReferences(filePath="...", line=X, character=Y)
```

**LSP Fallback**: If unavailable, use `codegraph_explore` first when codegraph_* tools exist; otherwise rely on explore agents + the ast-grep skill (`sg` CLI).

### Collect Background Results

```
// After main session analysis done, collect all task results
for each background task ID (`bg_...`): background_output(task_id="bg_...")
```

**Merge: bash + LSP + existing + explore findings. Mark "discovery" as completed.**

---

## Phase 2: Scoring & Location Decision

**Mark "scoring" as in_progress.**

### Scoring Matrix

| Factor | Weight | High Threshold | Source |
|--------|--------|----------------|--------|
| File count | 3x | >20 | bash |
| Subdir count | 2x | >5 | bash |
| Code ratio | 2x | >70% | bash |
| Unique patterns | 1x | Has own config | explore |
| Module boundary | 2x | Has index.ts/__init__.py | bash |
| Symbol density | 2x | >30 symbols | LSP |
| Export count | 2x | >10 exports | LSP |
| Reference centrality | 3x | >20 refs | LSP |

### Decision Rules

| Score | Action |
|-------|--------|
| **Root (.)** | ALWAYS create |
| **>15** | Create AGENTS.md |
| **8-15** | Create if distinct domain |
| **<8** | Skip (parent covers) |

### Output
```
AGENTS_LOCATIONS = [
  { path: ".", type: "root" },
  { path: "src/hooks", score: 18, reason: "high complexity" },
  { path: "src/api", score: 12, reason: "distinct domain" }
]
```

**Mark "scoring" as completed.**

---

## Phase 3: Generate AGENTS.md

**Mark "generate" as in_progress.**

<critical>
**File Writing Rule**: If AGENTS.md already exists at the target path → use `Edit` tool. If it does NOT exist → use `Write` tool.
NEVER use Write to overwrite an existing file. ALWAYS check existence first via `Read` or discovery results.
</critical>

### Root AGENTS.md (Full Treatment)

```markdown
# PROJECT KNOWLEDGE BASE

**Generated:** {TIMESTAMP}
**Commit:** {SHORT_SHA}
**Branch:** {BRANCH}

## OVERVIEW
{1-2 sentences: what + core stack}

## STRUCTURE
```
{root}/
├── {dir}/    # {non-obvious purpose only}
└── {entry}
```

## WHERE TO LOOK
| Task | Location | Notes |
|------|----------|-------|

## CODE MAP
{From LSP - skip if unavailable or project <10 files}

| Symbol | Type | Location | Refs | Role |
|--------|------|----------|------|------|

## CONVENTIONS
{ONLY deviations from standard}

## ANTI-PATTERNS (THIS PROJECT)
{Explicitly forbidden here}

## UNIQUE STYLES
{Project-specific}

## COMMANDS
```bash
{dev/test/build}
```

## NOTES
{Gotchas}
```

**Quality gates**: 50-150 lines, no generic advice, no obvious info.

### Subdirectory AGENTS.md (Parallel)

Launch writing tasks for each location:

```
for loc in AGENTS_LOCATIONS (except root):
  task(category="writing", load_skills=[], run_in_background=false, description="Generate AGENTS.md", prompt=`
    Generate AGENTS.md for: ${loc.path}
    - Reason: ${loc.reason}
    - 30-80 lines max
    - NEVER repeat parent content
    - Sections: OVERVIEW (1 line), STRUCTURE (if >5 subdirs), WHERE TO LOOK, CONVENTIONS (if different), ANTI-PATTERNS
  `)
```

**Wait for all. Mark "generate" as completed.**

---

## Phase 4: Review & Deduplicate

**Mark "review" as in_progress.**

For each generated file:
- Remove generic advice
- Remove parent duplicates
- Trim to size limits
- Verify telegraphic style

**Mark "review" as completed.**

---

## Final Report

```
=== init-deep Complete ===

Mode: {update | create-new}

Files:
  [OK] ./AGENTS.md (root, {N} lines)
  [OK] ./src/hooks/AGENTS.md ({N} lines)

Dirs Analyzed: {N}
AGENTS.md Created: {N}
AGENTS.md Updated: {N}

Hierarchy:
  ./AGENTS.md
  └── src/hooks/AGENTS.md
```

---

## Anti-Patterns

- **Static agent count**: MUST vary agents based on project size/depth
- **Sequential execution**: MUST parallel (explore + LSP concurrent)
- **Ignoring existing**: ALWAYS read existing first, even with --create-new
- **Over-documenting**: Not every dir needs AGENTS.md
- **Redundancy**: Child never repeats parent
- **Generic content**: Remove anything that applies to ALL projects
- **Verbose style**: Telegraphic or die
