init-deep

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.

On multi_agent_v2 sessions the same agent_type applies (the OMO installer exposes it) with fork_turns instead of fork_context. If a code block below conflicts with this section, this section wins.

When translating load_skills=[...], include the requested skill names in the spawned agent's 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/codegraph code map + 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

**TodoWrite ALL phases. Mark in_progress → completed in real-time.** ``` TodoWrite([ { id: "discovery", content: "Fire explore agents + LSP/codegraph map + 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" } ]) ```

---

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. Equip every agent with the code graph: any task touching structure, entry points, dependencies, or hotspots MUST query codegraph_* (explore/search/callers/callees/impact) and lsp_symbols when present, and ground its claims in that data instead of guessing from conventions. Richer real-graph context per agent = a more accurate project map.

// Fire all at once, collect results later
task(subagent_type="explore", load_skills=[], description="Explore project structure", run_in_background=true, prompt="Project structure: map real layout via codegraph_explore/codegraph_files → REPORT deviations from standard patterns")
task(subagent_type="explore", load_skills=[], description="Find entry points", run_in_background=true, prompt="Entry points: FIND main files, trace reach via codegraph_callees + lsp_symbols → 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/structure; codegraph_callers on core modules to see what is covered → REPORT unique conventions")

**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

# 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

Main Session: Concurrent Analysis

While background agents run, main session does:

1. Bash Structural Analysis

# 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. Code Map - drive LSP AND codegraph (do NOT skip)

Highest-signal source for the CODE MAP and the Symbol/Export/Reference scoring rows. Complementary, not alternatives - run BOTH when present, alongside the explore agents.

LSP - check lsp_status; model-facing names are lsp_status/lsp_symbols/lsp_find_references/lsp_goto_definition (some harnesses drop the lsp_ prefix):

• lsp_symbols scope="document" on each entry point -> file outline.
• lsp_symbols scope="workspace", query by kind (class/interface/function) -> symbol inventory.
• lsp_find_references on top exports (line/character from the symbols result) -> reference centrality.

codegraph - when codegraph_* tools exist (check codegraph_status); a first-class peer to LSP, NOT a last resort:

• codegraph_explore -> overview; codegraph_callers/codegraph_callees/codegraph_impact -> centrality + blast radius for the scoring matrix; codegraph_search/codegraph_files -> symbol/file inventory.

Only if NEITHER exists: explore agents + the ast-grep skill (sg), and mark centrality unmeasured in the CODE MAP.

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/codegraph + 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/cg
Export count	2x	>10 exports	LSP/cg
Reference centrality	3x	>20 refs	LSP/cg

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.

**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.

Root AGENTS.md (Full Treatment)

# 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/codegraph - skip only if neither exists 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 + codegraph 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