refactor: Update wiki index and logging templates to support agent protocols

templates/wiki-index.md

@@ -9,21 +9,35 @@ private: false
 # Master Index: {{GENOME_NAME}}
 
 **[AGENT INSTRUCTION]**
-Maintain strict alphabetical sorting within each section. Ensure the `last_updated` YAML field is modified upon every edit. Use only `[[slug]] - Summary` format.
+This is the primary navigation file. Read it first on every session before accessing individual pages.
+Maintain strict alphabetical sorting within each section.
+Update `last_updated` in the YAML frontmatter on every edit.
+Entry format: `- [[folder/slug]] — One-line summary. \`maturity: <value>\``
 
 ---
 
 ## Sources (`wiki/sources/`)
-*Ingested raw materials.*
+*Ingested raw materials. One entry per processed source.*
 
 
 ## Entities (`wiki/entities/`)
-*People, organizations, tools.*
+*People, organisations, tools, projects.*
 
 
 ## Concepts (`wiki/concepts/`)
-*Theories, methodologies, architecture.*
+*Theories, methodologies, patterns, architectural decisions.*
+
+
+## Queries (`wiki/queries/`)
+*Synthesised answers worth preserving. Archived explorations and analyses.*
+
+
+## Conflicts Pending Review (`wiki/queries/conflict-*.md`)
+*Created automatically when the agent detects contradictions between sources.*
+*Do not summarise entries here — list slugs only to avoid surfacing unresolved claims.*
+*Remove entry once the operator has resolved and closed the corresponding PR.*
 
 
 ## Private Synthesis (`wiki/private/`)
-*Restricted access. Use slug names ONLY. Do not append summaries to prevent metadata leakage.*
+*Restricted access. Requires `PRIVATE_CONTEXT: enabled` and unlocked repo.*
+*List slug names ONLY. Do not append summaries — prevents metadata leakage.*

templates/wiki-log.md

@@ -8,17 +8,47 @@ private: false
 # Operations Log: {{GENOME_NAME}}
 
 **[AGENT INSTRUCTION]**
-
-This is an append-only system ledger. Do not edit previous lines.
-
-Append new entries strictly using the following format:
-
-```text
-YYYY-MM-DD | [TYPE] | [AUTHOR] | Message
-```
-
-*(Valid TYPEs: INGEST, LINT, QUERY, CONFIG, SECURITY)*
+This is an append-only system ledger. Never edit or delete previous entries.
+Append new entries at the bottom using the format defined below.
 
 ---
 
-2024-05-08 | [CONFIG] | SYSTEM | Genome Scaffolded. Directory structure and encryption layer initialized.
+## Entry Format
+
+### Required header (enables shell parsing):
+```text
+## [YYYY-MM-DD] TYPE | Subject or title
+```
+
+### Required metadata block for all agent-generated entries:
+```markdown
+- run_id: `<short-uuid or session-identifier>`
+- model: `<model-name-and-version>`
+- context_read: `[[path/A]]`, `[[path/B]]`
+- output_written: `[[path/C]]`, `[[path/D]]`
+- reasoning: One sentence explaining what changed and why.
+```
+
+**Valid TYPEs:** `INGEST` | `LINT` | `QUERY` | `CONFLICT` | `CONFIG` | `SECURITY`
+
+**Parse examples:**
+```bash
+# Last 5 entries
+grep "^## \[" wiki/log.md | tail -5
+
+# All CONFLICT entries
+grep "^## \[" wiki/log.md | grep "CONFLICT"
+
+# All entries from a specific date
+grep "^## \[2026-05" wiki/log.md
+```
+
+---
+
+## [{{DATE}}] CONFIG | Genome scaffolded
+
+- run_id: `system-init`
+- model: `setup-knowledge-genome.sh`
+- context_read: *(none — initial scaffold)*
+- output_written: `[[wiki/index.md]]`, `[[wiki/log.md]]`, `[[AGENTS.md]]`
+- reasoning: Initial directory structure and encryption layer initialized by setup script.