/genesis

name: genesis
description: Initialize cortex vault — set up config, vault structure, and rebuild index
argument-hint: "[vault path, e.g. /srv/cortex or ~/cortex]"
allowed-tools:
  - Read
  - Write
  - Edit
  - Bash
  - Glob
  - Grep
  - AskUserQuestion

Initialize or reconfigure the cortex memory vault. Run once per machine, or again after switching machines to rebuild local state.

Steps

1. Check the cortex-vec CLI

Run `command -v cortex-vec`. If it is not on PATH, tell the user the vault's indexing and search need the CLI, and offer to install it now:

# Recommended: isolated tool install via uv
uv tool install cortex-vec

# Or with pip
pip install cortex-vec

If they decline, continue anyway — recording and the skills degrade gracefully — but note that semantic indexing and `cortex-vec` search stay unavailable until it is installed.

2. Check for existing config

Read `~/.cortex/config.json`. If it exists, show current config and ask if the user wants to reconfigure or abort.

3. Ask for vault path

If the user provided an argument, use that as the vault path. Otherwise, ask: "Where is the cortex vault? (e.g. /srv/cortex, ~/cortex)"

If the path exists and contains Notes/ or Projects/ or Raw/, recognize it as an existing vault. If the path doesn't exist, ask if they want to create it.

4. Ask for author info

Ask for:

• Author name (for git commits)
• Author email (for git commits)

5. Write config

Create `~/.cortex/` directory if needed, then write `~/.cortex/config.json`:

{
  "vault_path": "<user's answer>",
  "author": "<name>",
  "author_email": "<email>",
  "git": {
    "auto_commit": true,
    "auto_push": false,
    "commit_trailer": ""
  }
}

`git.commit_trailer` (string, optional, defaults to `""`): when non-empty, the distill and evolve skills append it as the last line of their commit messages, for git hosting setups that expect a specific trailer. Only those two commits, the ones that add new Notes / Projects pages, carry it; raw and broadcast commits do not.

The raw commit is also path-scoped (`git commit -- <paths>`: the Raw just written plus any snapshot reclaim removed), so it never carries what another session has staged in the shared vault index — a new page with a non-ASCII name, committed without the trailer, is exactly what a hosting secrets hook chokes on.

6. Initialize vault structure

Ensure these directories exist in the vault:

• `Raw/`
• `Notes/`
• `Projects/`

Those three are the whole taxonomy. Do **not** create `Weekly/` — it is no longer a Cortexes content type. If an existing vault already has a `Weekly/` directory, leave it and its files exactly where they are: never move, rewrite, or delete them. Tell the user it is no longer created, indexed, or searched, and that anything still worth keeping should be moved into `Notes/` or `Projects/` by hand, at their own pace.

Ensure `log.md` exists at the vault root. If missing, create it with:

---
created: <today>
---

# Cortex Log

Append-only record of vault operations (distill, evolve).

---
````

The file is append-only; do not overwrite if it exists.

### 7. Initialize git

If the vault is not a git repo, run `git init` and create an initial commit.

### 8. Rebuild _index.md

Scan every page under `Notes/<topic>/` and `Projects/<repo>/`, skipping any path
containing `_archive`. For each page extract the title, the tags from
frontmatter, and a one-line summary.

`Raw/` is deliberately NOT indexed — it is chronological and navigated by date,
so an index table would only duplicate the directory listing. A leftover
`Weekly/` is not indexed either, and is not listed in `_index.md`.

Write `<vault_path>/_index.md`. Both top-level sections group their rows into
`###` sub-sections — by topic under Notes, by repo under Projects — so the
index mirrors the on-disk layout:

```markdown
---
updated: <today>
---

# Cortex Index

## Projects

### <repo-name>

| Project | Tags | Summary |
|---------|------|---------|
| [[topic-title]] | tags | summary |

## Notes

### <topic>

| Note | Tags | Summary |
|------|------|---------|
| [[note-title]] | tags | summary |

Do NOT add an `entries:` count to the frontmatter. It is a derived value with no reader, and a hand-maintained copy of it drifts the moment a page is merged away or renamed. `cortex-vec status` reports the live count instead.

Legacy `Projects/<repo>/_index.md` files are not index rows — skip them. To check an existing index against the files on disk (and for the regex traps that make a naive check silently wrong), see `docs/index-audit.md`.

9. Show summary

Display:

✓ Cortex vault initialized
  Vault: <path>
  Config: ~/.cortex/config.json
  Author: <name> <email>
  Index: <N> pages in _index.md

  Next steps:
  - Sessions auto-record to Raw/ on exit
  - /cortexes:evolve → save notes or project info
  - /cortexes:distill → refine raw records
  - /cortexes:query → search your vault