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/skills/client-enrollment/SKILL.md

@@ -11,7 +11,7 @@ docs_update_checklist: [hosts_narrative_page_if_lxc_or_vm]
 Goal: bring a new host (workstation, LXC, VM) into inventory and the
 secrets model, with mesh membership only where it's actually needed.
 This wraps the existing `homelab client add` flow — see
-[operations/agent-enrollment.md](../../../operations/agent-enrollment.md) for
+[operations/agent-enrollment.md](../../operations/agent-enrollment.md) for
 the full walkthrough; this runbook is the risk/lifecycle framing.
 
 1. On any enrolled client: `homelab client add <hostname>` — appends a

.agents/skills/config-change-deploy/SKILL.md

@@ -18,7 +18,7 @@ own repo) and get it live, safely.
    `oikos/policy.yaml`.
 2. Clone/pull the `config_repo` (never edit the backend's working tree
    directly — tracked configs change by commit + push, per
-   [OIKOS.md](../../../OIKOS.md) conventions).
+   [OIKOS.md](../../OIKOS.md) conventions).
 3. Make the change, commit, push to `main`.
 4. The Gitea webhook fires the deploy pipeline for that repo (see
    [infrastructure/auto-deploy.md](../../../knowledge/wiki/infrastructure/auto-deploy.md) for

.agents/skills/incident-investigation/SKILL.md

@@ -23,7 +23,7 @@ Goal: understand what broke and why, before touching anything.
 5. Check the change ledger for recent mutations to the affected entity
    or anything upstream of it: `homelab service <name> history` (once
    populated) or grep `ledger/*.jsonl`.
-6. Write findings to a new `investigations/<date>-<slug>.md` — symptom,
+6. Write findings to a new `knowledge/sources/investigations/<date>-<slug>.md` — symptom,
    timeline, root cause, fix applied, prevention. This is the durable
    record; don't rely on chat history.
 

.agents/skills/runbook-dpkg-interrupted/SKILL.md

@@ -102,7 +102,7 @@ Then `systemctl status apt-recovery` from a fresh ssh to check progress.
 
 ## Related
 
-- [Operations cheatsheet](../../../operations/commands.md)
+- [Operations cheatsheet](../../operations/commands.md)
 - [Auto-deploy pipelines](../../../knowledge/wiki/infrastructure/auto-deploy.md)
 - [Hubris host page](../../../knowledge/wiki/hosts/hubris.md)