Merge branch 'release/1.0.0' into main

Makefile

@@ -1,5 +1,5 @@
 # =============================================================================
-# Knowledge Genome - Makefile v. 0.3.0
+# Knowledge Genome - Makefile v. 1.0.0
 # Orchestrates the setup and management of the knowledge base.
 # =============================================================================
 

templates/agents-genome.md

@@ -38,6 +38,7 @@ Session end or return to `disabled`: remind operator to run `git-crypt lock` on
 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.
 
 ### NEVER
 - Load `wiki/log.md` in full — read only the tail injected by the orchestrator.
@@ -58,10 +59,11 @@ Session end or return to `disabled`: remind operator to run `git-crypt lock` on
 
 Execute in this order before any file operation:
 
-1. Read `wiki/index.md` — full catalog of all pages and their maturity.
+1. **One source per session.** If multiple sources are queued in `raw/`, process only the first. Commit, close session. The orchestrator starts a new session for the next source.
-2. Read the last 20 log entries injected by orchestrator — do not open `wiki/log.md` directly.
+2. Read `wiki/index.md` — full catalog of all pages and their maturity.
-3. For any task involving related pages: `qmd search "<query>"` before opening files.
+3. Read the last 20 log entries injected by orchestrator — do not open `wiki/log.md` directly.
-4. Operate on individual target files. Never scan entire directories.
+4. For any task involving related pages: `qmd search "<query>"` before opening files.
+5. Operate on individual target files. Never scan entire directories.
 
 ---
 
@@ -77,7 +79,8 @@ Execute in this order before any file operation:
 5. Check each touched page for contradictions → apply §Conflict if found.
 6. Append entry to `wiki/index.md` (bottom of relevant section).
 7. Append log entry: `INGEST | <slug>`.
-8. Commit on `feat/ai-ingest-<slug>`. Open PR.
+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.
@@ -87,24 +90,28 @@ Execute in this order before any file operation:
 *Triggered by operator question.*
 
 1. `qmd search "<query>"` → identify candidate pages.
-2. Read relevant pages via `wiki/index.md` catalog.
+2. Read candidate pages directly.
 3. Synthesize answer with `[[wikilink]]` citations.
 4. If answer is non-trivial: save as `wiki/queries/<slug>.md`.
 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.*
+
 ### Lint
-*Triggered by operator or schedule.*
+*Triggered by operator with bash pre-scan output.*
 
-Find and report — do not auto-fix without operator approval:
+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.
 
-1. Orphan pages — no inbound `[[wikilink]]`.
+Agent tasks — apply semantic judgment to bash findings + independent semantic checks:
-2. Duplicate concepts — two pages covering same topic → propose merge.
-3. Implicit concepts — term in 3+ pages with no dedicated page.
-4. `maturity: draft` with 2+ sources → propose promote to `stable`.
-5. Broken internal links.
-6. Knowledge decay violations (§Decay).
 
+1. **Orphan pages** (list from bash): for each orphan, identify 1-3 existing pages that should link to it. Propose specific link additions.
+2. **Implicit concepts** (term list from bash): for each candidate term, determine if a dedicated page is warranted. If yes, draft stub.
+3. **Duplicate concepts**: `qmd search "<concept>"` for suspected duplicates → propose merge if confirmed.
+4. **`maturity: draft`** pages with 2+ sources cited → propose promote to `stable`.
+
+Report all findings as structured list. Do not modify files without operator approval.
 Append log entry: `LINT | <summary of findings>`.
 
 ---

templates/agents-master.md

@@ -86,48 +86,3 @@ Genome-level operations are governed by the genome's `AGENTS.md`, not this file.
    - Concepts in genome-X that should link to genome-Y but don't.
 3. Report findings. Do not modify any files.
 4. For each finding: create a conflict note in the genome where resolution belongs, following that genome's §Conflict procedure.
-
----
-
-## Reference Operations
-
-### Add a genome
-```bash
-make add-genome NAME=genome-newname DESC="Domain description"
-```
-Then update the architecture diagram in this file.
-
-### Sync submodules
-```bash
-make sync
-```
-
-### Update core-karpathy reference
-```bash
-git submodule update --remote core-karpathy
-git add core-karpathy
-git commit -m "chore: update core-karpathy to latest gist"
-git push
-```
-
-### Clone (full)
-```bash
-git clone --recurse-submodules \
-  {{FORGEJO_URL}}/{{FORGEJO_USER}}/{{MASTER_REPO}}.git
-```
-After cloning, unlock each genome on the host before starting an agent session.
-
-### Key rotation (emergency)
-If a key is compromised: `gcrypt_rotate_key "<genome>"` from project root.
-Update the Vaultwarden Secure Note with the new base64-encoded key.
-Revoke access from previous key holders.
-
-### Key registry
-
-| Genome | Vaultwarden Secure Note | Temp key file |
-|--------|------------------------|---------------|
-| genome-dev | `genome-dev key` | `keys/genome-dev.key` |
-| genome-finance | `genome-finance key` | `keys/genome-finance.key` |
-| genome-homelab | `genome-homelab key` | `keys/genome-homelab.key` |
-
-Temp key files in `keys/` are post-export only. Delete after upload to Vaultwarden.

templates/pr-description.md

@@ -0,0 +1,26 @@
+## Summary
+<!-- One sentence: goal of this session and source processed. -->
+
+## Pages Created
+| Path | Type | Maturity |
+|------|------|----------|
+| `[[folder/slug]]` | entity / concept / source / query | draft |
+
+## Pages Modified
+| Path | Change |
+|------|--------|
+| `[[folder/slug]]` | Added cross-reference to `[[other/page]]` |
+
+## Contradictions Found
+- [ ] None
+- [ ] `n` conflict file(s) created — listed below
+
+## Private Data Accessed
+- [ ] No — `PRIVATE_CONTEXT: disabled`
+- [ ] Yes — `PRIVATE_CONTEXT: enabled` · outputs in `wiki/private/` only
+
+## Scoped Lint (post-ingest)
+- [ ] Frontmatter valid on all touched pages
+- [ ] No broken wikilinks on touched pages
+- [ ] No issues found
+- [ ] Issues found (list):