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>

knowledge/wiki/infrastructure/mesh.md

@@ -117,7 +117,7 @@ Recipe for container-config changes (e.g. adding `extra_hosts`) on Portainer-man
 ## Changelog
 
 ### 2026-05-31 (later) — Authentik moved to the VPS; mesh-dependency for auth eliminated (supersedes the band-aid below)
-The earlier same-day fix routed `auth.hubris.network` through VPS Traefik → Caddy → LXC 124 **over the mesh**. That restored service but re-created the original fragility: if the mesh is dark when management restarts, the `192.168.8.175` backend is unreachable and management crash-loops again (the "Bootstrap note" in the entry below). That note is now **obsolete** — Authentik was migrated onto the VPS itself, so OIDC no longer touches the mesh. The `auth-authentik` → `192.168.8.175` route and its `skip-verify` transport were removed from `/opt/traefik-dynamic.yaml`; `auth.hubris.network` is now served by a local `authentik-server` container via Traefik Docker-provider labels, and netbird-mgmt has `depends_on: authentik-server: condition: service_healthy`. The socat / reverse-SSH bootstrap dance is no longer needed. Full detail: [2026-05-31 Authentik VPS migration](../../../investigations/archive/2026-05-31-authentik-vps-migration.md).
+The earlier same-day fix routed `auth.hubris.network` through VPS Traefik → Caddy → LXC 124 **over the mesh**. That restored service but re-created the original fragility: if the mesh is dark when management restarts, the `192.168.8.175` backend is unreachable and management crash-loops again (the "Bootstrap note" in the entry below). That note is now **obsolete** — Authentik was migrated onto the VPS itself, so OIDC no longer touches the mesh. The `auth-authentik` → `192.168.8.175` route and its `skip-verify` transport were removed from `/opt/traefik-dynamic.yaml`; `auth.hubris.network` is now served by a local `authentik-server` container via Traefik Docker-provider labels, and netbird-mgmt has `depends_on: authentik-server: condition: service_healthy`. The socat / reverse-SSH bootstrap dance is no longer needed. Full detail: [2026-05-31 Authentik VPS migration](../../sources/investigations/archive/2026-05-31-authentik-vps-migration.md).
 
 ### 2026-05-31 — Netbird mesh recovered; auth.hubris.network exposed via VPS Traefik