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>

tools/setup-hermes-soul.sh

@@ -14,7 +14,7 @@
 set -euo pipefail
 
 CONTEXT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
-HERMES_MD="$CONTEXT_DIR/HERMES.md"
+HERMES_MD="$CONTEXT_DIR/.agents/HERMES.md"
 SOUL_MD="${HOME}/.hermes/SOUL.md"
 
 # Colors for output (only when connected to a terminal)