docs: update AGENTS.md template for ingest skill and clarity

templates/agents-genome.md

@@ -3,7 +3,7 @@
 ## Identity
 
 | Field  | Value                                              |
-|--------|-------|
+| ------ | -------------------------------------------------- |
 | Genome | `{{GENOME_NAME}}`                                  |
 | Domain | `{{GENOME_DESC}}`                                  |
 | Owner  | `{{FORGEJO_USER}}`                                 |
@@ -55,6 +55,7 @@ Session end or return to `disabled`: remind operator to run `git-crypt lock` on
 8. Every PR must use `templates/pr-description.md`. Do not omit the tabular summary.
 
 ### NEVER
+
 - Load `wiki/log.md` in full — read only the tail injected by the orchestrator.
 - Rewrite `wiki/index.md` to reorder entries — append only; sorting is automated.
 - Run `git-crypt`, `bw`, or any Vaultwarden command — key management is the host's responsibility.
@@ -62,6 +63,7 @@ Session end or return to `disabled`: remind operator to run `git-crypt lock` on
 - Merge PRs — human approval required.
 
 ### ASK FIRST
+
 - Deleting any wiki page.
 - Changing `maturity` from `stable` to `deprecated`.
 - Writing to `wiki/private/` when PRIVATE_CONTEXT state is ambiguous.
@@ -84,7 +86,8 @@ Execute in this order before any file operation:
 ## Workflows
 
 ### Ingest
-*Triggered by new file in `raw/`.*
+
+_Triggered by new file in `raw/`._
 
 1. Read source once.
 2. Create `wiki/sources/<slug>.md` — summary + key points.
@@ -96,12 +99,14 @@ Execute in this order before any file operation:
 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):
+_Private source_ (`PRIVATE_CONTEXT: enabled` required):
+
 - All output → `wiki/private/<slug>.md` only.
 - PR title: `[PRIVATE] ingest: <slug>`.
 
 ### Query
-*Triggered by operator question.*
+
+_Triggered by operator question._
 
 1. `qmd search "<query>"` → identify candidate pages.
 2. Read candidate pages directly.
@@ -110,10 +115,11 @@ Execute in this order before any file operation:
 5. Append entry to `wiki/index.md` under Queries.
 6. Append log entry: `QUERY | <subject>`.
 
-*For general orientation without a specific query: read `wiki/index.md` directly.*
+_For general orientation without a specific query: read `wiki/index.md` directly._
 
 ### Lint
-*Triggered by operator with bash pre-scan output.*
+
+_Triggered by operator with bash pre-scan output._
 
 Pre-requisite: operator runs `bash scripts/lint-genomes.sh` and provides output to this session.
 The script handles deterministically: broken links, knowledge decay, page size, frontmatter validation.
@@ -133,6 +139,7 @@ Append log entry: `LINT | <summary of findings>`.
 ## File Conventions
 
 ### Frontmatter
+
 Required on every wiki page:
 
 ```yaml
@@ -152,19 +159,25 @@ private: true | false
 - `deprecated` — superseded. Add `> **DEPRECATED:** <reason>` callout at top of body.
 
 ### Links
+
 - Internal: `[[folder/file]]` — Obsidian wikilinks only. Never `[text](url)` for internal refs.
 - Cross-genome: `[[../genome-target/wiki/folder/file]]`.
 - External: `[text](https://...)`.
 
 ### Index entries
+
 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.
 
 ### Log entries
+
 Append one entry per operation to `wiki/log.md`:
+
 ```markdown
 ## [YYYY-MM-DD] TYPE | Subject
 
@@ -174,6 +187,7 @@ Append one entry per operation to `wiki/log.md`:
 - output_written: `[[path/C]]`
 - reasoning: One sentence — what changed and why.
 ```
+
 Valid TYPEs: `INGEST` `LINT` `QUERY` `CONFLICT` `CONFIG` `SECURITY`
 
 Parse: `grep "^## \[" wiki/log.md | tail -5`
@@ -197,16 +211,20 @@ last_updated: YYYY-MM-DD
 private: false
 ---
 ```
+
 ```markdown
 ## Conflict: <concept>
 
 **Claim A (existing):** [[path/to/existing-page]]
+
 > Summary of current wiki position.
 
 **Claim B (new):** [[path/to/new-source]]
+
 > Summary of contradicting evidence.
 
 **Assessment:**
+
 - Confidence A: high | medium | low — <reason>
 - Confidence B: high | medium | low — <reason>
 - Recommendation: `accept_b` | `keep_a` | `requires_human_review`
@@ -226,9 +244,11 @@ private: false
 - `maturity: draft` not updated in **90 days** → flag during lint.
 
 Flagged pages: prepend to body:
+
 ```markdown
 > **⚠️ STALE:** Last validated {{last_updated}}. Re-validation required.
 ```
+
 Propose re-validation task. Do not change `maturity` without new source evidence.
 
 ---
@@ -236,7 +256,7 @@ Propose re-validation task. Do not change `maturity` without new source evidence
 ## Collaboration
 
 | Role           | Access            | Permitted                                                                            |
-|------|--------|-----------|
+| -------------- | ----------------- | ------------------------------------------------------------------------------------ |
 | Owner          | Full — key holder | Read/write everywhere                                                                |
 | Collaborator   | No key            | Push to `raw/articles`, `raw/transcripts`, `raw/code-packs`, `raw/assets`            |
 | Local AI agent | Conditional       | `private/` only when `PRIVATE_CONTEXT: enabled`                                      |