docs: streamline & consolidate the tree (phase 6)

Problem: after the wiki-hq reorg, agent-instruction and human-doc domains
were still scattered across the repo root, with three now-redundant stub
files cluttering it. The organizing principle wasn't visible in the layout.

Change — enforce three clear buckets:
- .agents/  = how agents operate: OIKOS.md, HERMES.md (moved from root),
  shared/ conventions, domains/ schemas, skills/, and operations/ (operator
  cheatsheet + enrollment + hermes-agent, moved from root).
- knowledge/ = what exists + evidence: wiki/, GLOSSARY.md, and sources/ now
  including investigations/ (incident records are evidence/sources).
- root = substrate + two entry points (AGENTS.md, README.md), plus plans/
  as its own design-intent domain.

Moves:
- investigations/ -> knowledge/sources/investigations/ (incl. archive/, index).
- operations/ -> .agents/operations/.
- HERMES.md -> .agents/HERMES.md.
- Deleted unreferenced root stubs CAVEMAN.md, CONTRIBUTING.md, and OIKOS.md
  (its 7 remaining linkers repointed to .agents/OIKOS.md).

Consumers updated:
- inventory.yaml doc_page (agent-enrollment) + regenerated hosts/*.yaml + cards.
- tools/setup-hermes-soul.sh and bootstrap.sh (x2) -> .agents/HERMES.md.
- bin/homelab help string -> .agents/operations/hermes-agent.md.
- knowledge/operations schemas, llm-wiki, page-templates, incident-investigation
  skill, AGENTS.md/README nav -> new investigations/operations paths.
- All markdown links rewritten via the path-resolving mapper.

Left in place (substrate/executable/separate-domain): hosts/, ledger/, tools/,
plans/, oikos/, mcp/, secrets/, bin/, inventory.yaml.

Verification: docs-lint at baseline (2 intentional cross-repo refs, no new
breakage); gen-topology.py --check exit 0; build_host_files.py idempotent; all
doc_page targets resolve; Hermes provisioning scripts point at the new path.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

.agents/domains/operations/schema.md

@@ -5,6 +5,11 @@ procedures), investigations (incident evidence), and plans (design docs for non-
 follows [writing-style](../../shared/writing-style.md); runbooks and plans use the imperative voice
 exception.
 
+Where each kind lives: runbooks are skills under [`.agents/skills/`](../../skills/); operator
+reference (command cheatsheet, enrollment, Hermes agent) lives in
+[`.agents/operations/`](../../operations/); investigations are sources under
+`knowledge/sources/investigations/`; plans stay in the repo-root `plans/` folder (below).
+
 ## Plans always live in `plans/`
 
 **Any plan or design doc for the Homelab is written into the repo `plans/` folder as
@@ -39,12 +44,12 @@ transition: "<from> -> <to>"   # only for lifecycle runbooks
 
 ## Investigations
 
-Incident records live in `investigations/YYYY-MM-DD-slug.md` and are **evidence sources** — written
+Incident records live in `knowledge/sources/investigations/YYYY-MM-DD-slug.md` and are **evidence sources** — written
 once at incident time, then linked from the changelogs of the nodes they implicate. Sections:
 `## Summary`, `## Timeline`, `## Root cause`, `## Mitigations applied`, `## Open questions`. Resolved
-incidents move to `investigations/archive/`.
+incidents move to `knowledge/sources/investigations/archive/`.
 
 ## The operations log
 
-`plans/log.md` and `investigations/log.md` are append-only records of documentation operations on
+`plans/log.md` and `knowledge/log.md` are append-only records of documentation operations on
 those areas (`## [YYYY-MM-DD] <op> | <summary>`), distinct from the Oikos change ledger.