cortex-init

A setup workflow for Cortex, a routing layer that connects an agent to the tools and systems already in use. It scans the local environment and creates a personalised Workflow Registry.

In plain words
What is it for?
Discovering installed agents, skills, commands, servers, plugins, hooks, and related configuration files, then using that information to build Cortex's registry.
Why use it?
It helps Cortex fit an existing stack without replacing systems or overwriting the user's configuration without confirmation.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/amitvijapur/cortex/cortex-init
Any agent
npx skills add amitvijapur/cortex --skill cortex-init
Clone the repo
git clone --depth 1 https://github.com/amitvijapur/cortex

Made for: Claude Code, Codex.

Per session 61 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 885 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00061 $0.00885
Opus 5 $0.00030 $0.00443
Sonnet 5 $0.00012 $0.00177
Haiku 4.5 $0.00006 $0.00089

Measured 2d ago against content hash e348b84c6975, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

cortex-init scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/cortex-init/SKILL.md · 70 lines

How it starts

The opening of the file, as written. The whole thing — 70 lines — stays where its author put it; the contents beside it link to each section on GitHub.

cortex-init — adopt the user's existing stack into Cortex

Cortex is a routing layer. This skill wires it around whatever the user already runs, instead of imposing a fixed toolset. Their systems are preserved and tied together — nothing is replaced, and their cortex.md is never overwritten without a backup and their confirmation.

Run these steps in order.

1. Discover — deterministic scan

Run the scanner:

python3 ~/.claude/bin/cortex init

It writes <state-dir>/cortex-inventory.json and prints a summary. Read the JSON. It lists their agents (counted by division), skills, commands, MCP servers, hooks, plugins, detected other-agent config files (Cursor / Codex / Gemini / Aider / Windsurf), and relevant CLIs on PATH.

2. Interview — fill gaps, don't interrogate

Auto-accept the obvious; only ask what you genuinely cannot infer. Keep it to a handful of questions. Ask about:

  • Grouping: large pools (e.g. "262 agents across 21 divisions") — one "Specialist Agents" pool, or break out a few they reach for often?
  • Category for any MCP/tool you can't classify from its name (search? database? scraping? design? docs?).
  • Defaults per task class — for build, review, plan, research, debug, design, which of their systems is the go-to? Offer a sensible guess and let them correct it.
  • Exclusions — anything detected that they do not want Cortex to route to.

Use their answers, not assumptions.

3. Synthesize the registry

Write a Workflow Registry in the exact shape Cortex uses (mirror the ## Workflow Registry section of the installed cortex.md). For each system / agent-group / skill-family / MCP:

  • Installed: Yes
  • Strengths: one line
  • Best for: one line
  • a small pattern table — | Pattern | Use When |

Then draft a Decision Shortcuts table (task type → default route → tier) from the defaults they gave you. Ground every entry in what the scan actually found — never invent a tool they don't have.

Read the full file on GitHub · 70 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2d ago First seen · 70 lines · 61 tokens per session scan A e348b84c6975

Subscribe to this mod's changes

cortex-init is a skill published in the GitHub repository amitvijapur/cortex (5 stars, last pushed 2d ago), licensed MIT. It adds 61 tokens to every session and 885 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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