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>
Problem: runbooks are agent-executable procedures but lived at the repo root,
separate from the other agent instruction now under .agents/.
Change:
- Move runbooks/<name>.md -> .agents/skills/<name>/SKILL.md (folder per skill,
matching the wiki-hq skills layout). Frontmatter (name, risk_class, inputs,
verification, docs_update_checklist, transition) preserved.
- Rewrite links (inbound from plans; between-skill siblings) via the move map.
- Update prose references in AGENTS.md, HERMES.md, .agents/OIKOS.md, and the
operations schema; fix a pre-existing stale link to operations/commands.md.
No code consumed runbooks/ by path, so nothing else changes.
Verification: all SKILL.md frontmatter parses with valid risk_class; every
lifecycle transition resolves to an oikos/ontology.yaml state; broken-link
count 127 -> 126 (fixed one, introduced none).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
