docs: Overhaul README and consolidate operational docs

templates/agents-master.md

@@ -86,48 +86,3 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
    - Concepts in genome-X that should link to genome-Y but don't.
 3. Report findings. Do not modify any files.
 4. For each finding: create a conflict note in the genome where resolution belongs, following that genome's §Conflict procedure.
-
----
-
-## Reference Operations
-
-### Add a genome
-```bash
-make add-genome NAME=genome-newname DESC="Domain description"
-```
-Then update the architecture diagram in this file.
-
-### Sync submodules
-```bash
-make sync
-```
-
-### Update core-karpathy reference
-```bash
-git submodule update --remote core-karpathy
-git add core-karpathy
-git commit -m "chore: update core-karpathy to latest gist"
-git push
-```
-
-### Clone (full)
-```bash
-git clone --recurse-submodules \
-  {{FORGEJO_URL}}/{{FORGEJO_USER}}/{{MASTER_REPO}}.git
-```
-After cloning, unlock each genome on the host before starting an agent session.
-
-### Key rotation (emergency)
-If a key is compromised: `gcrypt_rotate_key "<genome>"` from project root.
-Update the Vaultwarden Secure Note with the new base64-encoded key.
-Revoke access from previous key holders.
-
-### Key registry
-
-| Genome | Vaultwarden Secure Note | Temp key file |
-|--------|------------------------|---------------|
-| genome-dev | `genome-dev key` | `keys/genome-dev.key` |
-| genome-finance | `genome-finance key` | `keys/genome-finance.key` |
-| genome-homelab | `genome-homelab key` | `keys/genome-homelab.key` |
-
-Temp key files in `keys/` are post-export only. Delete after upload to Vaultwarden.