Makefile

@@ -1,5 +1,5 @@
 # =============================================================================
-# Knowledge Genome - Makefile v. 1.1.4
+# Knowledge Genome - Makefile v. 1.1.3
 # Orchestrates the setup and management of the knowledge base.
 # =============================================================================
 

README.md

@@ -1020,9 +1020,14 @@ and keep the wiki atomically navigable.
 
 ### Linking conventions
 
-- **Intra-genome:** `[[folder/file]]` — Obsidian wikilinks only.
+| Type                   | Format                                      |
-- **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.
+| ---------------------- | ------------------------------------------- |
-- **External:** `[text](https://...)` — standard Markdown.
+| Internal (same genome) | `[[folder/slug]]` — Obsidian wikilinks only |
+| 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

@@ -27,10 +27,6 @@ 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-orchestrator/genome-dev
+#   cd ~/knowledge-genome-setup/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="${HOME}/knowledge-genome-orchestrator"
+WORK_DIR="${HOME}/knowledge-genome-setup"
 KEYS_DIR="${WORK_DIR}/keys"
 TEMPLATES_DIR="${PROJECT_ROOT}/templates"
 LIB_DIR="${PROJECT_ROOT}/lib"

scripts/setup-genomes.sh

@@ -48,9 +48,6 @@ for entry in "${GENOMES[@]}"; do
         # Initial genome push
         git add .
         git commit -m "feat: initial scaffold and git-crypt init for ${GENOME_NAME}"
-
-        git branch -M main
-
         git push -u origin main
 
         # Key export and instructions

scripts/setup-master.sh

@@ -37,7 +37,5 @@ scaffold_master "."
 git add .
 git commit -m "chore: initialize master scaffold" || info "No changes to commit in master."
 
-git branch -M main
-
 # 3. Initial Push
 git push -u origin main

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-orchestrator/lib \
+#   KG_LIB_DIR=/opt/knowledge-genome-setup/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

@@ -47,12 +47,12 @@ Session end or return to `disabled`: remind operator to run `git-crypt lock` on
 
 1. `raw/` is read-only. Never create, modify, or delete files in `raw/`.
 2. `wiki/` is agent-owned. Create, update, and maintain all wiki pages here.
-3. Every operation → one log entry appended to `wiki/log.md` (§Log) (automated via manifest during Ingest).
+3. Every operation → one log entry appended to `wiki/log.md` (§Log).
-4. Every new page → one entry appended to `wiki/index.md` (§Index) (automated via manifest during Ingest).
+4. Every new page → one entry appended to `wiki/index.md` (§Index).
 5. Never commit to `main`. Branch per task; PR required; no self-merge.
 6. Contradict, don't overwrite. New evidence contradicts existing claim → §Conflict.
 7. Never commit plaintext to any path marked for encryption in `.gitattributes`.
-8. Every PR must use `templates/pr-description.md`. Do not omit the tabular summary (automated via run-ingest.sh during Ingest).
+8. Every PR must use `templates/pr-description.md`. Do not omit the tabular summary.
 
 ### NEVER
 
@@ -89,23 +89,18 @@ Execute in this order before any file operation:
 
 _Triggered by new file in `raw/`._
 
-**Phase 1 — Semantic Pass (Agent Skill)**
 1. Read source once.
 2. Create `wiki/sources/<slug>.md` — summary + key points.
 3. Per entity (person, tool, org): create or update `wiki/entities/<name>.md`.
 4. Per concept (pattern, theory, decision): create or update `wiki/concepts/<name>.md`.
 5. Check each touched page for contradictions → apply §Conflict if found.
-6. **Final action:** Write `.ingest-manifest.json` at the genome root.
+6. Append entry to `wiki/index.md` (bottom of relevant section).
-7. **STOP.** Do not proceed to index, log, lint, commit, or PR — these are Phase 2.
+7. Append log entry: `INGEST | <slug>`.
-
+8. Run scoped lint on pages created or modified in this session. Report issues in PR description. Do not auto-fix.
-**Phase 2 — Deterministic Post-Processing (`run-ingest.sh`)**
+9. Commit on `feat/ai-ingest-<slug>`. Open PR using `templates/pr-description.md`.
-_Executed automatically by the orchestrator after Phase 1._
-8. Append entry to `wiki/index.md` (bottom of relevant section).
-9. Append log entry: `INGEST | <slug>`.
-10. Run scoped lint on pages created or modified in this session. Report issues in PR description. Do not auto-fix.
-11. Commit on `feat/ai-ingest-<slug>`. Open PR using `templates/pr-description.md`.
 
 _Private source_ (`PRIVATE_CONTEXT: enabled` required):
+
 - All output → `wiki/private/<slug>.md` only.
 - PR title: `[PRIVATE] ingest: <slug>`.
 
@@ -171,20 +166,16 @@ private: true | false
 
 ### Index entries
 
-> **Skill mode:** auto-generated by `run-ingest.sh` from manifest. Below applies to manual workflows only.
-
 Append at bottom of relevant section in `wiki/index.md`:
 
 ```
 - [[folder/slug]] — One-line summary. `maturity: draft`
 ```
 
-Never reorder. Alphabetical sorting is handled by the post-processor (index-append.py); the pre-commit hook only enforces the security policy.
+Never reorder. Alphabetical sort is handled by the pre-commit hook.
 
 ### Log entries
 
-> **Skill mode:** auto-generated by `run-ingest.sh` from manifest. Below applies to manual workflows only.
-
 Append one entry per operation to `wiki/log.md`:
 
 ```markdown

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 discoveries routed to target raw/ · zero stale submodule-relative wikilinks.
+**Metrics:** no cross-genome boundary violations · submodule pointers current · cross-genome wikilinks valid · no private data outside local network.
 
 ---
 
@@ -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 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.
+3. Cross-genome references use relative wikilinks only: `[[../genome-target/wiki/folder/page]]`.
 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.
 
@@ -59,7 +59,6 @@ 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
@@ -80,58 +79,14 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
 
 ---
 
-## Cross-Genome Pull (Navigation Skill)
+## Cross-Genome Lint
 
-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.
+_Manual, monthly — requires operator initiation. Not automated._
 
-### How it works
+1. Use `qmd search "<concept>"` to find pages covering the same concept across genomes.
-
+2. Identify:
-Three actors, mirroring the ingest two-phase split:
+   - Concepts defined in 2+ genomes with potentially conflicting definitions.
-
+   - Entities referenced across genomes without a canonical cross-genome wikilink.
-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.
+   - Concepts in genome-X that should link to genome-Y but don't.
-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. Report findings. Do not modify any files.
-3. **Target ingest.** The working genome's own standard pipeline processes that raw → PR → human gate. Same gate as any other source.
+4. For each finding: create a conflict note in the genome where resolution belongs, following that genome's §Conflict procedure.
-
-### 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.
-
-```markdown
-> 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.

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 by the post-processor (index-append.py); the pre-commit hook only enforces the security policy.
+Alphabetical sorting is handled automatically by the pre-commit hook.
 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: <value>\``
 
 ---