docs(R5): rewrite knowledge schema + llm-wiki for DB-native model; deprecate root inventory.yaml
Rewrote .agents/domains/knowledge/schema.md and .agents/shared/llm-wiki.md
which described the deleted Python substrate (bin/homelab, oikos/cards/,
oikos/ledger.py, root inventory.yaml, knowledge/sources/, get_page/
search_docs MCP tools). Now reflect ADR 0003: Postgres DB is the single
source of truth for structured data and narrative knowledge; seeds/*.yaml
are bootstrap+DR manifests (content-hashed via seed_versions); archive/
knowledge/ is the frozen legacy wiki; MCP search_knowledge/get_entity_
knowledge replace get_page/search_docs.
Swept substrate refs in .agents/shared/{writing-style,page-templates}.md
and .agents/domains/operations/schema.md: bare inventory.yaml ->
seeds/inventory.yaml; knowledge/sources/ -> archive/knowledge/sources/
(historical); get_changelog/oikos/ledger.py -> DB audit trail / structured
document changelog field; HERMES -> Nomos.
Root inventory.yaml (618-line Python-era file superseded 2026-07-07 by
seeds/inventory.yaml) replaced with a deprecation stub pointing to the seed
and DB. Kept as a stub rather than deleted because AGENTS.md §1/§2 still
point clients at /opt/homelab-context/inventory.yaml; full on-client path
reconciliation deferred to R13.
Flagged export gap: oikos export regenerates seeds/{ontology,inventory,
policy}.yaml but NOT seeds/knowledge.yaml — API-added knowledge lives only
in the DB until hand-edited into the seed.
VERSION 0.7.7 -> 0.7.8. Plan R5 marked done.
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@@ -36,7 +36,7 @@ Every doc-level page follows the same shape so a reader scans it in one pass.
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1. **One H1 = the page title.** Node pages use `# <id> — \`<name>\``; topic pages use `# <Topic>`.
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2. **Opening definition.** First paragraph, 1–3 sentences, says what the thing is. No motivation, no marketing, no setup.
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3. **Body sections** in the natural order for the topic. Reuse the section templates in [page-templates.md](page-templates.md).
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4. **`## Changelog`** at the bottom of every node/topic page — reverse-chronological, append-only. This section is machine-parsed (Go MCP `get_changelog` in `internal/mcp/server.go`); keep the `### YYYY-MM-DD — title` shape.
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4. **`## Changelog`** at the bottom of every node/topic page — reverse-chronological, append-only. This section is stored as a structured field on the `document` entity in the DB; keep the `### YYYY-MM-DD — title` shape so it parses cleanly.
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5. **Related links** only at the bottom, only when a reference cannot be woven inline.
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## Section indexes (folder READMEs)
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@@ -53,12 +53,12 @@ duplicated prose, no narrative between the intro and the table.
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- Prefer **tables** for enumerable items with internal structure (service/port maps, field lists, status grids). Reserve bullets for short non-structured lists.
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- Use the **bold-leading-phrase pattern** for structured points: `**Read-only by construction.** The MCP server never mutates state.` — a bold noun phrase, a period, then the explanation.
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- When enumerating across services or nodes, give each its own `###` sub-section or a table row, not one run-on paragraph.
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- Use backticks for code, paths, hostnames, and file names (`inventory.yaml`, `192.168.8.77`, `pct config`); italics for first-mention terminology.
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- Use backticks for code, paths, hostnames, and file names (`seeds/inventory.yaml`, `192.168.8.77`, `pct config`); italics for first-mention terminology.
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- Use `>` blockquotes for caveats and gaps that interrupt the main flow: `> **Outstanding gap.** DNS-vs-inventory drift check not yet wired.` One thought per blockquote.
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## Diagrams
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- Mermaid is the default for topology and flow diagrams. `infrastructure/topology.md` is generated by `oikos/gen-topology.py` — do not hand-edit it. (Go DB-native topology generation planned.)
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- Mermaid is the default for topology and flow diagrams. `infrastructure/topology.md` in the archived wiki was generated by the retired `oikos/gen-topology.py`; the DB-native equivalent is a future task — do not hand-edit the archived file expecting it to regenerate.
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- ASCII box diagrams are fine for small shape diagrams; keep them to one screen.
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## Sourcing and cross-references
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