knowledge-genome-orchestrator/templates/agents-master.md

SYSTEM DIRECTIVE — {{MASTER_REPO}}

Identity

Field	Value
Repo	{{MASTER_REPO}}
Owner	{{FORGEJO_USER}}
Remote	{{FORGEJO_URL}}/{{FORGEJO_USER}}/{{MASTER_REPO}}

Role: Cross-genome coordinator for the Knowledge Genome network. Metrics: no cross-genome boundary violations · submodule pointers current · cross-genome discoveries routed to target raw/ · zero stale submodule-relative wikilinks.

---

Architecture

{{MASTER_REPO}}/
├── core-karpathy/      ← Reference pattern — read-only, never modify
├── genome-example/     ← Submodule placeholder (replace with your domain)
└── AGENTS.md

Each genome has its own AGENTS.md with domain-specific rules. Genome-level operations are governed by the genome's AGENTS.md, not this file.

---

Global Security Rules

PRIVATE_CONTEXT scope

• Toggle is per-genome and per-session. Enabling for genome-finance does NOT enable for genome-dev.
• Cloud LLM models: PRIVATE_CONTEXT must be disabled for all genomes. Private data never leaves the local network.

Log sanitization

• Never print decrypted secrets, session tokens, or key contents to stdout or log files.
• Document only run_id and genome name — never the key value.

Key management

• Key injection is the host's responsibility — executed before this session starts.
• Never write, suggest, or generate scripts that save .key files to disk.

---

Immutable Rules

1. Operate within ONE genome at a time. No atomic commits across multiple genomes.
2. core-karpathy is read-only. Never commit to it.
3. Cross-genome references are NEVER expressed as wikilinks. When a concept belongs to another genome, use the navigation skill to emit a raw stub into that genome's raw/articles/ and let its own ingest pipeline handle it asynchronously.
4. Never commit to main in any genome. PRs required; no self-merge.
5. Per-genome AGENTS.md governs all wiki operations within that genome. This file governs boundaries only.

NEVER

• Load multiple wiki/index.md files simultaneously for cross-genome comparison — use qmd.
• Run git-crypt, bw, or Vaultwarden commands — host responsibility.
• Modify files in more than one genome in the same operation.
• Create cross-genome wikilinks (e.g., [[../genome-*/wiki/...]]). All cross-domain connections must be routed via the navigation skill as raw stubs.
• Modify core-karpathy in any way.

ASK FIRST

• Any operation that touches two or more genomes.
• Updating submodule pointers in master.
• Any key rotation procedure.
• Enabling PRIVATE_CONTEXT — operator must confirm git-crypt unlock ran on host.

---

Session Start

1. Identify which genome(s) this session involves.
2. Read the relevant genome's wiki/index.md — not all genomes' indexes.
3. For cross-genome discovery: qmd search "<concept>" across the multi-genome index.
4. Operate on one genome at a time. Switch genome only when the previous operation is committed.

---

Cross-Genome Pull (Navigation Skill)

Cross-genome knowledge moves by pull, never push: the genome you are working in draws material in; nothing is ever written into another genome. The cross-genome reading is performed by a deterministic collector outside any agent's context, so the agent still operates within ONE genome (Immutable Rule 1 holds). The cross_source registry flag decides which genomes may be read as sources.

How it works

Three actors, mirroring the ingest two-phase split:

1. Collector (collect-crossgen.sh, deterministic, agent-free). Clones each genome flagged cross_source: yes read-only at its remote HEAD — a disposable checkout, for freshness; never the pinned submodule state. Reads each wiki/index.md plus the relevant pages and assembles a dossier of excerpts with provenance (source genome, page, date/commit). Writes nothing to any source genome.
2. Synthesis (agent, navigation skill, read/edit only). Reads only the dossier — a single artifact inside the working genome's context — then the skill deposits one abstract, non-private raw into the working genome at raw/articles/crossgen-<topic>-<YYYY-MM-DD>.md, and STOPS.
3. Target ingest. The working genome's own standard pipeline processes that raw → PR → human gate. Same gate as any other source.

When to pull

Pull is initiated deliberately (operator- or context-driven, never on a timer). Produce a crossgen raw ONLY when all three hold:

1. Ownership elsewhere. The concept, entity, or pattern is defined and maintained in another genome, and you need it framed for the working domain.
2. Structural relevance. It influences decisions, patterns, or entities here — not a casual mention.
3. No fresh local coverage. qmd search "<concept>" in the working genome returns nothing, or only a stub that needs enrichment.

If in doubt, do NOT pull. A missed cross-reference is cheaper than crossgen spam.

Boundaries (enforced by the master)

• Sources are restricted to cross_source: yes genomes. A genome flagged no (e.g., a client / confidential file) is NEVER read as a source — the collector skips it physically. The wall decides what may flow; it does not rely on the agent's discipline.
• Sources are read-only, at HEAD. No write, commit, branch, or PR in any genome other than the one being worked on.
• NEVER git submodule update --remote. Read other genomes via disposable read-only clones — never by moving this master's submodule pointers (that is ASK FIRST).
• NEVER read */private/*. The skill runs PRIVATE_CONTEXT: disabled and private/ is an encrypted blob; even on an unlocked host, private paths are off-limits.
• Confidential / client genomes are normally isolated from cross-genome pulls entirely (operator policy). Whatever genome a pull runs into, the output raw must be abstract and non-private.

Output raw (the only artifact written)

Path (in the working genome): raw/articles/crossgen-<topic>-<YYYY-MM-DD>.md Plain text. No YAML frontmatter (raw is immutable input). No wikilinks of any kind — never a [[../genome-*/...]] path.

> Cross-genome pull | Into: genome-<working> | Sources: genome-<a> (wiki/concepts/x.md), genome-<b> (wiki/entities/y.md) | HEAD: <short-sha…> | Date: YYYY-MM-DD

# <Topic> (synthesized from other genomes)

## What the source genomes say
[Abstract, faithful synthesis of the relevant material. Plain text, no private data, no wikilinks.]

## Relevance to this genome
[Why it matters in the working domain; textual references to existing local entities, if any.]

## Suggested local action
[Semantic hint for this genome's ingest: e.g., create/update wiki/concepts/<concept>.md, map local relationships.]

Rules:

• Each pull writes a new, dated crossgen file — never overwrite or edit an existing raw (raw is immutable). Deduplication happens later, at the wiki level: the working genome's normal ingest reconciles against existing pages via its §Conflict procedure.
• The raw is processed by the working genome's standard ingest as an ordinary raw/articles/ source — no special path.
• The collector and the raw deposit are the deterministic side of the skill; the agent only synthesizes content. Agents never create, modify, or delete files in any raw/ directly.