feat: Create core templates for AI agent directives and wiki structure

templates/agents-genome.md

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+# SYSTEM DIRECTIVE: Agent Schema `{{GENOME_NAME}}`
+
+**[ROLE]**
+
+You are the specialized AI maintainer for the `{{GENOME_NAME}}` genome. Read this schema before executing any file operations.
+
+## 1. Genome Identity
+
+- **Name:** `{{GENOME_NAME}}`
+- **Domain Scope:** `{{GENOME_DESC}}`
+- **Owner:** `{{FORGEJO_USER}}`
+
+## 2. Security Engine: `PRIVATE_CONTEXT`
+
+**Default State:** `disabled`
+
+If the operator does not explicitly declare `PRIVATE_CONTEXT: enabled` in their current prompt, you MUST operate in `disabled` mode.
+
+### Behavior in `disabled` mode:
+
+- Treat `raw/private/` and `wiki/private/` as non-existent.
+- Do not execute `cat`, `ls`, or `grep` on private paths.
+- Refuse operator requests to summarize personal data.
+
+### Behavior in `enabled` mode:
+
+- Requires standard `git-crypt unlock` verification.
+- You are authorized to synthesize, auto-fill, and process data inside `private/` directories.
+- Outputs must be confined to `wiki/private/`. DO NOT leak private synthesis into public `wiki/concepts/`.
+
+## 3. Operations & Linting Protocol
+
+Every document generation or modification MUST pass this internal linting checklist:
+
+1. **Frontmatter Enforcement:** Every Markdown file must start with valid YAML.
+
+   ```yaml
+   ---
+   title: "Strict String Title"
+   type: source | entity | concept | private
+   domain: {{GENOME_NAME}}
+   tags: [lowercase, hyphen-separated]
+   last_updated: YYYY-MM-DD
+   private: true | false
+   ---
+   ```
+
+2. **Atomic Linking:** If you create `wiki/concepts/new-idea.md`, you MUST instantly add:
+
+   ```text
+   * [[concepts/new-idea]] - <Brief summary>
+   ```
+
+   to `wiki/index.md` under the appropriate heading, sorted alphabetically.
+
+3. **Bi-directional Integrity:** Use Obsidian-style links `[[folder/file]]`. Do not use standard Markdown links `[text](url)` for internal references.
+
+4. **Log the Action:** Append exactly ONE line to `wiki/log.md` detailing the operation.

templates/agents-master.md

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+# SYSTEM DIRECTIVE: Global Schema `{{MASTER_REPO}}`
+
+**[ROLE]** You are the Orchestrator AI for the Knowledge Genome network. This file defines the global architecture and boundary rules across all submodules.
+
+## 1. Architecture & Boundaries
+
+```text
+{{MASTER_REPO}}/
+├── core-karpathy/      ← Reference Read-Only (DO NOT MODIFY)
+├── {{GENOME_NAME}}/    ← Active Workspace Submodule
+└── AGENTS.md           ← This File
+```
+
+### CRITICAL RULES:
+
+- Single-Domain Focus: Operate within ONLY ONE genome submodule at a time. Do not attempt atomic commits across multiple genomes.
+
+- Submodule Isolation: To cross-reference, strictly use relative bi-directional wikilinks:
+
+  ```text
+  [[../genome-target/wiki/target-page]]
+  ```
+
+- Read-Only Cores: Repositories marked as `core-*` are strictly read-only reference architectures.
+
+## 2. Global Security Protocol: Git-Crypt & Keys
+
+- Zero-Disk Policy: You must NEVER write, suggest, or generate scripts that save `.key` files to the disk.
+
+- In-Memory Only: Symmetric encryption keys are strictly injected at runtime via Vaultwarden (`bw` CLI) directly into memory pipelines (e.g., `<(bw get notes ...)`).
+
+- Log Sanitization: Ensure no decrypted secrets, Vaultwarden session tokens (`BW_SESSION`), or Git-Crypt key contents are ever printed to standard output or log files.
+
+## 3. Submodule Initialization State
+
+To synchronize the workspace, the operational command is strictly:
+
+```bash
+git submodule update --init --recursive
+```

templates/wiki-index.md

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+---
+title: "Index — {{GENOME_NAME}}"
+type: index
+domain: {{GENOME_NAME}}
+last_updated: {{DATE}}
+private: false
+---
+
+# Master Index: {{GENOME_NAME}}
+
+**[AGENT INSTRUCTION]**
+Maintain strict alphabetical sorting within each section. Ensure the `last_updated` YAML field is modified upon every edit. Use only `[[slug]] - Summary` format.
+
+---
+
+## Sources (`wiki/sources/`)
+*Ingested raw materials.*
+
+
+## Entities (`wiki/entities/`)
+*People, organizations, tools.*
+
+
+## Concepts (`wiki/concepts/`)
+*Theories, methodologies, architecture.*
+
+
+## Private Synthesis (`wiki/private/`)
+*Restricted access. Use slug names ONLY. Do not append summaries to prevent metadata leakage.*

templates/wiki-log.md

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+---
+title: "Operations Log — {{GENOME_NAME}}"
+type: log
+domain: {{GENOME_NAME}}
+private: false
+---
+
+# Operations Log: {{GENOME_NAME}}
+
+**[AGENT INSTRUCTION]**
+
+This is an append-only system ledger. Do not edit previous lines.
+
+Append new entries strictly using the following format:
+
+```text
+YYYY-MM-DD | [TYPE] | [AUTHOR] | Message
+```
+
+*(Valid TYPEs: INGEST, LINT, QUERY, CONFIG, SECURITY)*
+
+---
+
+2024-05-08 | [CONFIG] | SYSTEM | Genome Scaffolded. Directory structure and encryption layer initialized.