Files
claude-engineering-plugin/docs/specs/codex.md
Trevin Chow b290690655 fix: research agents prefer native tools over shell for repo exploration
Research agents (repo-research-analyst, git-history-analyzer,
best-practices-researcher, framework-docs-researcher) were using
shell commands like find, rg, cat, and chained pipelines for routine
codebase exploration. This triggers permission prompts in Claude Code
and degrades the user experience when these agents run as sub-agents.

Updated all research agents with platform-agnostic tool selection
guidance that prefers native file-search/glob, content-search/grep,
and file-read tools over shell equivalents. Shell is now reserved for
commands with no native equivalent (ast-grep, bundle show, git).
Git-history-analyzer additionally limits shell to one simple git
command per call with no chaining or piping.

Added tool selection rules to AGENTS.md so future agents follow
the same pattern by default.
2026-03-16 22:25:00 -07:00

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# Codex Spec (Config, Prompts, Skills, MCP)
Last verified: 2026-01-21
## Primary sources
```
https://developers.openai.com/codex/config-basic
https://developers.openai.com/codex/config-advanced
https://developers.openai.com/codex/custom-prompts
https://developers.openai.com/codex/skills
https://developers.openai.com/codex/skills/create-skill
https://developers.openai.com/codex/guides/agents-md
https://developers.openai.com/codex/mcp
```
## Config location and precedence
- Codex reads local settings from `~/.codex/config.toml`, shared by the CLI and IDE extension. citeturn2view0
- Configuration precedence is: CLI flags → profile values → root-level values in `config.toml` → built-in defaults. citeturn2view0
- Codex stores local state under `CODEX_HOME` (defaults to `~/.codex`) and includes `config.toml` there. citeturn4view0
## Profiles and providers
- Profiles are defined under `[profiles.<name>]` and selected with `codex --profile <name>`. citeturn4view0
- A top-level `profile = "<name>"` sets the default profile; CLI flags can override it. citeturn4view0
- Profiles are experimental and not supported in the IDE extension. citeturn4view0
- Custom model providers can be defined with base URL, wire API, and optional headers, then referenced via `model_provider`. citeturn4view0
## Custom prompts (slash commands)
- Custom prompts are Markdown files stored under `~/.codex/prompts/`. citeturn3view0
- Custom prompts require explicit invocation and arent shared through the repository; use skills to share or auto-invoke. citeturn3view0
- Prompts are invoked as `/prompts:<name>` in the slash command UI. citeturn3view0
- Prompt front matter supports `description:` and `argument-hint:`. citeturn3view0turn2view3
- Prompt arguments support `$1``$9`, `$ARGUMENTS`, and named placeholders like `$FILE` provided as `KEY=value`. citeturn2view3
- Codex ignores non-Markdown files in the prompts directory. citeturn2view3
## AGENTS.md instructions
- Codex reads `AGENTS.md` files before doing any work and builds a combined instruction chain. citeturn3view1
- Discovery order: global (`~/.codex`, using `AGENTS.override.md` then `AGENTS.md`) then project directory traversal from repo root to CWD, with override > AGENTS > fallback names. citeturn3view1
- Codex concatenates files from root down; files closer to the working directory appear later and override earlier guidance. citeturn3view1
## Skills (Agent Skills)
- A skill is a folder containing `SKILL.md` plus optional `scripts/`, `references/`, and `assets/`. citeturn3view3turn3view4
- `SKILL.md` uses YAML front matter and requires `name` and `description`. citeturn3view3turn3view4
- Required fields are single-line with length limits (name ≤ 100 chars, description ≤ 500 chars). citeturn3view4
- At startup, Codex loads only each skills name/description; full content is injected when invoked. citeturn3view3turn3view4
- Skills can be repo-scoped in `.agents/skills/` and are discovered from the current working directory up to the repository root. User-scoped skills live in `~/.agents/skills/`. citeturn1view1turn1view4
- Inference: some existing tooling and user setups still use `.codex/skills/` and `~/.codex/skills/` as legacy compatibility paths, but those locations are not documented in the current OpenAI Codex skills docs linked above.
- Codex also supports admin-scoped skills in `/etc/codex/skills` plus built-in system skills bundled with Codex. citeturn1view4
- Skills can be invoked explicitly using `/skills` or `$skill-name`. citeturn3view3
## MCP (Model Context Protocol)
- MCP configuration lives in `~/.codex/config.toml` and is shared by the CLI and IDE extension. citeturn3view2turn3view5
- Each server is configured under `[mcp_servers.<server-name>]`. citeturn3view5
- STDIO servers support `command` (required), `args`, `env`, `env_vars`, and `cwd`. citeturn3view5
- Streamable HTTP servers support `url` (required), `bearer_token_env_var`, `http_headers`, and `env_http_headers`. citeturn3view5