Agent anatomy

Skill bowtiefunnel/bowtie-funnel-Labs/skills/agent-anatomy

Reusable skills for AI coding agents. Organize any agent folder into a clean, filesystem-first layout.

Install

npx -y skills add bowtiefunnel/bowtie-funnel-Labs --skill agent-anatomy

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Use when scaffolding a new AI agent's project folder, or when an existing agent's files (prompt, tools, procedures, scheduled jobs, integrations) are scattered in one directory with no structure. Organizes any agent folder into a filesystem-first layout.

SKILL.md

3.6 KB, as published. Nobody here has run it

agent-anatomy

Organize any AI agent's project into a filesystem-first layout: one agent = one folder, every capability = a file in a conventionally-named subfolder. Language-agnostic — tools can be Python, TypeScript, anything.

Core principle: names come from file paths, not config. tools/issue_refund.py is the tool issue_refund. Never add a name: field to restate the path.

The convention

instructions.md (the always-on system prompt) is the one required file. Everything else is an optional, canonically-named subfolder. Classify each file:

A file that…	goes in	notes
is the system prompt / persona / instructions	`instructions.md`	rename `prompt.txt`, `system.md`, etc. to this
does a discrete action the agent invokes	`tools/`	filename = tool name
is a markdown procedure followed on demand	`skills/`	e.g. `how-to-escalate.md`
runs on a timer / cron / "every morning"	`schedules/`
receives inbound messages (webhook, bot)	`channels/`	Slack, HTTP, Discord
calls an outbound third-party API / service	`connections/`	external APIs, MCP servers
is a nested agent	`subagents/<name>/`	recurse — same convention
is durable state the agent reads back	`memory/`
is shared code imported by tools/jobs	`lib/`	utils/formatters — not a capability
is dev scratch / TODOs / personal notes	leave in place	flag it, don't move

Two modes — detect first

Empty or missing folder → Scaffold. Has files → Reorganize.

Scaffold

Ask once: what does this agent do? (purpose + capabilities)
Write a real instructions.md for that purpose — not a placeholder.
Create only the subfolders that purpose needs, each with one real starter file (a working tool stub, a procedure, etc.).

Reorganize

Inventory every file. Skip .git/, node_modules/, .venv/, lockfiles, build output.
Classify each against the table.

Present a move plan as a table, then STOP for approval:

current path        →  new path                   reason
prompt.txt          →  instructions.md            system prompt (required file)
refund_tool.py      →  tools/issue_refund.py      discrete action; path = tool name
how_to_escalate.md  →  skills/how-to-escalate.md  on-demand procedure
daily_report.py     →  schedules/daily_report.py  cron job
slack.py            →  channels/slack.py          inbound channel
utils.py            →  lib/utils.py               shared helper, not a capability
notes.txt           →  (leave in place)           dev scratch — ask first

Apply only after approval. Then move the files.

Hard rules

Never delete anything. Reorganizing is moving, not removing.
Never move without an approved plan (reorganize mode).
No empty folders — a subfolder exists only once it holds a real file.
Exact folder names only — skills/ not knowledge/, schedules/ not jobs/, channels/ not integrations/. Inventing synonyms defeats a shared convention.
The prompt is always instructions.md — rename any variant to it.
No name: fields duplicating the path.
Inside a git repo, move with git mv. Never overwrite an existing destination — flag the collision in the plan instead.