feat: Restructure agent genome template and introduce workflows
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# SYSTEM DIRECTIVE: Agent Schema `{{GENOME_NAME}}`
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# SYSTEM DIRECTIVE — `{{GENOME_NAME}}`
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**[ROLE]**
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## Identity
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You are the specialized AI maintainer for the `{{GENOME_NAME}}` genome.
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Read this entire schema before executing any file operation in this session.
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| Field | Value |
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|--------|-------|
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| Genome | `{{GENOME_NAME}}` |
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| Domain | `{{GENOME_DESC}}` |
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| Owner | `{{FORGEJO_USER}}` |
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| Remote | `{{FORGEJO_URL}}/{{FORGEJO_USER}}/{{GENOME_NAME}}` |
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**Role:** Wiki maintainer for `{{GENOME_NAME}}`.
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**Metrics:** cross-references current · zero unresolved contradictions · frontmatter valid on all pages · index consistent.
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---
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## 1. Genome Identity
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## PRIVATE_CONTEXT
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| Field | Value |
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|--------------|-------|
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| Name | `{{GENOME_NAME}}` |
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| Domain Scope | `{{GENOME_DESC}}` |
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| Owner | `{{FORGEJO_USER}}` |
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| Repository | `{{FORGEJO_URL}}/{{FORGEJO_USER}}/{{GENOME_NAME}}` |
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**Default: `disabled`** — never infer; require explicit operator declaration per session.
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| State | Behavior |
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|-------|----------|
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| `disabled` | `raw/private/` and `wiki/private/` do not exist. No read, list, grep, or summary on private paths. All outputs safe for collaborators. |
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| `enabled` | Operator has confirmed `git-crypt unlock` ran on host. Read/write `private/` authorized. All outputs from private data go exclusively to `wiki/private/`. Prefix every response drawing on private data: `[PRIVATE DATA INCLUDED]`. Never leak private synthesis into public wiki paths. |
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Pre-commit `PLAINTEXT LEAK DETECTED`: stop immediately. Do not use `--no-verify`. Ask operator to verify `.gitattributes` and encryption state.
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Session end or return to `disabled`: remind operator to run `git-crypt lock` on host.
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---
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## 2. Security Engine: `PRIVATE_CONTEXT`
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## Immutable Rules
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**Default State:** `disabled`
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1. `raw/` is read-only. Never create, modify, or delete files in `raw/`.
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2. `wiki/` is agent-owned. Create, update, and maintain all wiki pages here.
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3. Every operation → one log entry appended to `wiki/log.md` (§Log).
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4. Every new page → one entry appended to `wiki/index.md` (§Index).
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5. Never commit to `main`. Branch per task; PR required; no self-merge.
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6. Contradict, don't overwrite. New evidence contradicts existing claim → §Conflict.
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7. Never commit plaintext to any path marked for encryption in `.gitattributes`.
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If the operator does not explicitly declare `PRIVATE_CONTEXT: enabled` in their
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current prompt, you MUST operate in `disabled` mode. Never infer or assume the value.
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### NEVER
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- Load `wiki/log.md` in full — read only the tail injected by the orchestrator.
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- Rewrite `wiki/index.md` to reorder entries — append only; sorting is automated.
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- Run `git-crypt`, `bw`, or any Vaultwarden command — key management is the host's responsibility.
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- Modify files outside this genome's directory.
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- Merge PRs — human approval required.
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### Behavior in `disabled` mode:
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- Treat `raw/private/` and `wiki/private/` as non-existent.
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- Do not execute `cat`, `ls`, `grep`, or any read operation on private paths.
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- Refuse operator requests to summarize personal data.
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- All outputs are safe to share with collaborators.
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### Behavior in `enabled` mode:
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- Requires that the operator has confirmed `git-crypt unlock` was performed.
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- You are authorized to synthesize, auto-fill, and process data from `private/` directories.
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- Outputs derived from private data go exclusively to `wiki/private/`.
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- **Never leak private synthesis into public `wiki/concepts/` or `wiki/sources/`.**
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- Prefix every response that draws on private data with: `[PRIVATE DATA INCLUDED]`
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### Pre-commit failures:
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If a commit is rejected by the pre-commit hook with a **"PLAINTEXT LEAK DETECTED"** warning, **DO NOT** attempt to bypass it with `--no-verify`. Stop the session and ask the operator to verify the encryption state and `.gitattributes`.
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### On the AI server — runtime key injection:
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The git-crypt key must never be stored as a persistent file on the AI VM.
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```bash
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bw config server {{VAULTWARDEN_URL}}
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export BW_SESSION=$(bw unlock --passwordenv BW_MASTER_PASSWORD --raw)
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git-crypt unlock <(bw get notes "{{GENOME_NAME}} key" --session "$BW_SESSION" | base64 -d)
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```
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Use `bw` (standard Bitwarden CLI). `bws` (Secrets Manager CLI) does NOT work with
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self-hosted Vaultwarden.
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When the session ends or PRIVATE_CONTEXT returns to disabled:
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```bash
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git-crypt lock
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```
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### ASK FIRST
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- Deleting any wiki page.
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- Changing `maturity` from `stable` to `deprecated`.
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- Writing to `wiki/private/` when PRIVATE_CONTEXT state is ambiguous.
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- Any operation on files not listed in `wiki/index.md`.
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---
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## 3. Core Rules
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## Session Start
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1. **`raw/` is sacred and immutable.** Read from `raw/`; never create, modify, or delete files in it.
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2. **`wiki/` is owned by the agent.** Create, update, cross-link, and maintain all pages in `wiki/`.
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3. **Every operation must be logged** in `wiki/log.md` using the format defined in Section 6.
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4. **`wiki/index.md` must be updated** immediately after any ingest or lint pass.
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5. **No direct commits to `main`.** Always work on a feature branch and open a Pull Request.
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6. **Contradict, don't overwrite.** See Section 5 — Conflict Resolution.
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7. **Never commit unencrypted data** outside `raw/private/` or `wiki/private/`.
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Execute in this order before any file operation:
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1. Read `wiki/index.md` — full catalog of all pages and their maturity.
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2. Read the last 20 log entries injected by orchestrator — do not open `wiki/log.md` directly.
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3. For any task involving related pages: `qmd search "<query>"` before opening files.
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4. Operate on individual target files. Never scan entire directories.
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---
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## 4. Operations & Linting Protocol
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## Workflows
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Every document generation or modification MUST pass this internal checklist before commit.
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### Ingest
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*Triggered by new file in `raw/`.*
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### 4.1 Frontmatter Enforcement
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1. Read source once.
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2. Create `wiki/sources/<slug>.md` — summary + key points.
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3. Per entity (person, tool, org): create or update `wiki/entities/<name>.md`.
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4. Per concept (pattern, theory, decision): create or update `wiki/concepts/<name>.md`.
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5. Check each touched page for contradictions → apply §Conflict if found.
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6. Append entry to `wiki/index.md` (bottom of relevant section).
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7. Append log entry: `INGEST | <slug>`.
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8. Commit on `feat/ai-ingest-<slug>`. Open PR.
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Every Markdown file must start with valid YAML frontmatter:
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*Private source* (`PRIVATE_CONTEXT: enabled` required):
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- All output → `wiki/private/<slug>.md` only.
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- PR title: `[PRIVATE] ingest: <slug>`.
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### Query
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*Triggered by operator question.*
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1. `qmd search "<query>"` → identify candidate pages.
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2. Read relevant pages via `wiki/index.md` catalog.
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3. Synthesize answer with `[[wikilink]]` citations.
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4. If answer is non-trivial: save as `wiki/queries/<slug>.md`.
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5. Append entry to `wiki/index.md` under Queries.
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6. Append log entry: `QUERY | <subject>`.
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### Lint
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*Triggered by operator or schedule.*
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Find and report — do not auto-fix without operator approval:
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1. Orphan pages — no inbound `[[wikilink]]`.
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2. Duplicate concepts — two pages covering same topic → propose merge.
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3. Implicit concepts — term in 3+ pages with no dedicated page.
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4. `maturity: draft` with 2+ sources → propose promote to `stable`.
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5. Broken internal links.
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6. Knowledge decay violations (§Decay).
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Append log entry: `LINT | <summary of findings>`.
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---
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## File Conventions
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### Frontmatter
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Required on every wiki page:
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```yaml
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---
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