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).
-4. Every new page → one entry appended to `wiki/index.md` (§Index) (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).
 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.
-7. **STOP.** Do not proceed to index, log, lint, commit, or PR — these are Phase 2.
-
-**Phase 2 — Deterministic Post-Processing (`run-ingest.sh`)**
-_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`.
+6. Append entry to `wiki/index.md` (bottom of relevant section).
+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.
+9. 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>`.
 
@@ -171,8 +166,6 @@ 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`:
 
 ```
@@ -183,8 +176,6 @@ 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