feat(cross-genome): Implement pull-based navigation skill and policy

README.md

@@ -1020,14 +1020,9 @@ and keep the wiki atomically navigable.
 
 ### Linking conventions
 
-| Type                   | Format                                      |
+- **Intra-genome:** `[[folder/file]]` — Obsidian wikilinks only.
-| ---------------------- | ------------------------------------------- |
+- **Cross-genome:** NOT supported via wikilink. Submodule pointers make relative paths brittle. When a concept belongs to another genome, use the navigation skill to emit a raw stub into that genome's `raw/articles/` directory so its local ingest pipeline can process it.
-| Internal (same genome) | `[[folder/slug]]` — Obsidian wikilinks only |
+- **External:** `[text](https://...)` — standard Markdown.
-| Cross-genome           | `[[../genome-target/wiki/folder/slug]]`     |
-| External               | `[text](https://url)` — standard Markdown   |
-
-Never use `[text](relative/path)` for internal references. Obsidian wikilinks are
-bidirectional and appear in the graph view.
 
 ### Log format
 

lib/deps.sh

@@ -27,6 +27,10 @@ check_deps() {
   if ! command -v bw &>/dev/null; then
     warn "Optional tool 'bw' (Bitwarden CLI) not found. Vaultwarden integration will be manual."
   fi
+
+  if ! command -v python3 &>/dev/null; then
+    warn "Optional tool 'python3' not found. Needed for 'make test' and the ingest skill (index-append.py), not for setup."
+  fi
 }
 
 check_git_identity() {

lib/git-crypt.sh

@@ -55,7 +55,7 @@ gcrypt_verify() {
 #
 # USAGE:
 #   source lib/git-crypt.sh
-#   cd ~/knowledge-genome-setup/genome-dev
+#   cd ~/knowledge-genome-orchestrator/genome-dev
 #   gcrypt_rotate_key "genome-dev"
 #
 # REQUIRES:

registry.sh

@@ -12,7 +12,7 @@ _REGISTRY_LOADED=1
 PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Dynamic paths
-WORK_DIR="${HOME}/knowledge-genome-setup"
+WORK_DIR="${HOME}/knowledge-genome-orchestrator"
 KEYS_DIR="${WORK_DIR}/keys"
 TEMPLATES_DIR="${PROJECT_ROOT}/templates"
 LIB_DIR="${PROJECT_ROOT}/lib"

skills/ingest/scripts/scoped-lint.sh

@@ -4,7 +4,7 @@
 # Run the framework's validation on ONLY the files touched this session.
 # Reuses lib/lint.sh + lib/output.sh — same checks as `make lint`, scoped.
 #
-#   KG_LIB_DIR=/opt/knowledge-genome-setup/lib \
+#   KG_LIB_DIR=/opt/knowledge-genome-orchestrator/lib \
 #     scoped-lint.sh <genome_name> wiki/sources/x.md wiki/entities/y.md
 #
 # Exits non-zero if any hard error is found, so the agent notices.

templates/agents-genome.md

@@ -179,7 +179,7 @@ Append at bottom of relevant section in `wiki/index.md`:
 - [[folder/slug]] — One-line summary. `maturity: draft`
 ```
 
-Never reorder. Alphabetical sort is handled by the pre-commit hook.
+Never reorder. Alphabetical sorting is handled by the post-processor (index-append.py); the pre-commit hook only enforces the security policy.
 
 ### Log entries
 

templates/agents-master.md

@@ -9,7 +9,7 @@
 | 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 wikilinks valid · no private data outside local network.
+**Metrics:** no cross-genome boundary violations · submodule pointers current · cross-genome discoveries routed to target raw/ · zero stale submodule-relative wikilinks.
 
 ---
 
@@ -50,7 +50,7 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
 
 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 use relative wikilinks only: `[[../genome-target/wiki/folder/page]]`.
+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.
 
@@ -59,6 +59,7 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
 - 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
@@ -79,14 +80,64 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
 
 ---
 
-## Cross-Genome Lint
+## Cross-Genome Pull (Navigation Skill)
 
-_Manual, monthly — requires operator initiation. Not automated._
+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.
 
-1. Use `qmd search "<concept>"` to find pages covering the same concept across genomes.
+### How it works
-2. Identify:
+
-   - Concepts defined in 2+ genomes with potentially conflicting definitions.
+Three actors, mirroring the ingest two-phase split:
-   - Entities referenced across genomes without a canonical cross-genome wikilink.
+
-   - Concepts in genome-X that should link to genome-Y but don't.
+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.
-3. Report findings. Do not modify any files.
+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-&lt;topic&gt;-&lt;&lt;YYYY-MM-DD&gt;.md`, and STOPS.
-4. For each finding: create a conflict note in the genome where resolution belongs, following that genome's §Conflict procedure.
+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 "&lt;concept&gt;"` 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-&lt;topic&gt;-&lt;&lt;YYYY-MM-DD&gt;.md`
+Plain text. No YAML frontmatter (raw is immutable input). **No wikilinks of any kind** — never a `[[../genome-*/...]]` path.
+
+```markdown
+&gt; Cross-genome pull | Into: genome-&lt;working&gt; | Sources: genome-&lt;a&gt; (wiki/concepts/x.md), genome-&lt;b&gt; (wiki/entities/y.md) | HEAD: &lt;short-sha…&gt; | Date: YYYY-MM-DD
+```
+
+# &lt;Topic&gt; (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/&lt;concept&gt;.md, map local relationships.]
+
+---
+
+- 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.
+
+---
+
+That closes the remaining audit items for `agents-master.md`. The file is now fully pull-oriented and consistent with the dossier.

templates/wiki-index.md

@@ -12,9 +12,9 @@ private: false
 **[AGENT INSTRUCTION]**
 This is the primary navigation file. Read it first on every session before accessing individual pages.
 Append new entries at the bottom of the relevant section — do not reorder or rewrite sections.
-Alphabetical sorting is handled automatically by the pre-commit hook.
+Alphabetical sorting is handled by the post-processor (index-append.py); the pre-commit hook only enforces the security policy.
 Update `last_updated` in the YAML frontmatter on every edit.
-Entry format: `- [[folder/slug]] — One-line summary. \`maturity: <value>\``
+Entry format: `- [[folder/slug]] — One-line summary. \`maturity: &lt;value&gt;\``
 
 ---