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/hosts/hubris.md

@@ -8,7 +8,7 @@ workloads still live here. As of 2026-07-01, hubris is node 1 of the 2-node
 ## At a glance
 - **Role:** Proxmox VE 9.1.2 hypervisor (kernel `6.14.11-4-pve`)
 - **Hardware:** GMKtec NucBox M6 Ultra — AMD Ryzen 5 7640HS (Phoenix APU), 12 vCPU / ~28 GiB RAM, 2× Samsung 990 EVO Plus NVMe (one SSD primary, one for `library` LVM). 2× Realtek RTL8125 NICs (`r8169`).
-- **BIOS:** 1.02 (2025-08-06) — vendor not on LVFS, no automated update path. See [investigations](../../../investigations/archive/2026-04-21-hubris-crash-loop.md).
+- **BIOS:** 1.02 (2025-08-06) — vendor not on LVFS, no automated update path. See [investigations](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md).
 - **Uplink:** `vmbr1` (slave: `eno1`) → SODOLA switch → Fritz!Box 7590. DHCP-reserved `192.168.178.10/24`, gateway `192.168.178.1`.
 - **Homelab bridge:** `vmbr0` — portless internal bridge, `192.168.8.77/24` + `192.168.8.1/24` alias (LXC default gateway). All 16 LXCs and the HAOS VM are on `vmbr0`. Proxmox routes between `vmbr0` and `vmbr1`; Fritz!Box has a static route `192.168.8.0/24 → 192.168.178.10`.
 - **WiFi:** disabled 2026-06-02 — `wlp3s0` removed from `/etc/network/interfaces`, wpa config deleted. Was used as a failover to the now-retired Slate AX AP.
@@ -113,8 +113,8 @@ OpenSSH on `0.0.0.0:22`. Netbird's built-in SSH server is on `100.122.38.109:220
 - [Media permissions](../infrastructure/media-permissions.md)
 - [Monitoring](../infrastructure/monitoring.md)
 - [Backups (disabled)](../infrastructure/backups.md)
-- [Operations cheatsheet](../../../operations/commands.md)
-- [Investigation: 2026-04-21 crash loop](../../../investigations/archive/2026-04-21-hubris-crash-loop.md)
+- [Operations cheatsheet](../../../.agents/operations/commands.md)
+- [Investigation: 2026-04-21 crash loop](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md)
 - [strong — Proxmox host](strong.md)
 
 ## Changelog
@@ -138,7 +138,7 @@ User destroyed the heaper LXC. No `116.conf.bak` left behind in `/etc/pve/lxc/`.
 `/etc/sysctl.d/99-bbr.conf` switches `net.ipv4.tcp_congestion_control` from `cubic` to `bbr` and `net.core.default_qdisc` from `fq_codel` to `fq`. Also bumps `rmem_max`/`wmem_max` to 64 MiB and widens `tcp_rmem`/`tcp_wmem`. `tcp_bbr` module pinned at boot via `/etc/modules-load.d/bbr.conf`. Triggered by Nextcloud client downloads from a WiFi laptop pulling ~2 MB/s despite a 152 Mbps link — server-side baseline through Caddy with BBR is ~400 MB/s single-stream loopback, so any client-perceived single-stream improvement is pure congestion-control win. Touches every LXC's outbound TCP since they all share this kernel.
 
 ### 2026-04-29 — relocated to better-ventilated spot
-User physically moved the host to a new location with improved airflow. Post-move idle baseline (45 min uptime, light load): k10temp Tctl **47.2 °C**, amdgpu edge 42 °C, nvme0 composite 34.9 °C / sensor1 32.9 °C, nvme1 composite 38.9 °C / sensor1 52.9 °C, DRAM 34–35.5 °C, ACPI zone 47–49 °C. Compares well against the 2026-04-23 thermal-pad steady-state (nvme0 sensor1 60–61 °C). Watch the lifetime NVMe warning-time counter over the coming days for confirmation. See [investigation](../../../investigations/archive/2026-04-21-hubris-crash-loop.md#2026-04-29-physical-relocation).
+User physically moved the host to a new location with improved airflow. Post-move idle baseline (45 min uptime, light load): k10temp Tctl **47.2 °C**, amdgpu edge 42 °C, nvme0 composite 34.9 °C / sensor1 32.9 °C, nvme1 composite 38.9 °C / sensor1 52.9 °C, DRAM 34–35.5 °C, ACPI zone 47–49 °C. Compares well against the 2026-04-23 thermal-pad steady-state (nvme0 sensor1 60–61 °C). Watch the lifetime NVMe warning-time counter over the coming days for confirmation. See [investigation](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md#2026-04-29-physical-relocation).
 
 ### 2026-04-28 — Phase 1 WiFi failover
 Host now dual-homed: LAN `192.168.8.77` (primary) + WiFi `192.168.8.141` (failover, metric 200) on the GL-AXT1800-714-5G AP. Installed `wpasupplicant`+`iw`; added `wlp3s0` stanza to `/etc/network/interfaces` with `wpa-conf`; ARP isolation sysctls in `post-up`. Built `wan-failover.service` to remove the vmbr0 default route on `eno1` carrier loss, since the bridge's carrier doesn't follow `eno1` (the LXC veths keep it `1`). LXC/VM guests are still LAN-only — Phase 2 will migrate them.
@@ -147,10 +147,10 @@ Host now dual-homed: LAN `192.168.8.77` (primary) + WiFi `192.168.8.141` (failov
 This wiki created. Live state at this date: 14 LXCs running (109 syncthing stopped), 1 VM, kernel `6.14.11-4-pve`, uptime 3 d 0 h post drive-removal A/B test. Compared to memory snapshot from a week ago, **destroyed**: LXC 100 (yunohost arr), 106 (flaresolverr), 107 (marimo), 110 (photoprism), 111 (karakeep), 112 (immich), 115 (reticulum). 100 + 106 destroyed per the planned 2026-04-21 \*arr migration retention; the others removed since.
 
 ### 2026-04-23 — SSD cooling + thermal pads installed
-Thermal pads on both NVMe drives. Steady-state nvme0 composite 47 °C / sensor1 60–61 °C, nvme1 38–40 °C. Zero new warning-time minutes after install. Watch the lifetime warning-time counter going forward, not absolute sensor1. See [investigation](../../../investigations/archive/2026-04-21-hubris-crash-loop.md#2026-04-23-thermal-pad-verdict).
+Thermal pads on both NVMe drives. Steady-state nvme0 composite 47 °C / sensor1 60–61 °C, nvme1 38–40 °C. Zero new warning-time minutes after install. Watch the lifetime warning-time counter going forward, not absolute sensor1. See [investigation](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md#2026-04-23-thermal-pad-verdict).
 
 ### 2026-04-22 — drive removal A/B test
-Removed external USB backup drive (Silicon Motion `090c:2320`). Disabled the four `backup-library*.timer` units, commented the fstab entry. Goal: confirm whether the drive + UAS interaction on the AMD USB4 PCIe tunnel is the dominant root cause of the silent hard-locks. Pre-drive uptime was 33 days; with drive, repeated crashes despite UAS blacklist + mount-on-demand. **Result so far:** 3+ days uptime — the drive looks like the primary contributor; `cpu-epp` remains as belt-and-suspenders thermal protection. See [investigation](../../../investigations/archive/2026-04-21-hubris-crash-loop.md).
+Removed external USB backup drive (Silicon Motion `090c:2320`). Disabled the four `backup-library*.timer` units, commented the fstab entry. Goal: confirm whether the drive + UAS interaction on the AMD USB4 PCIe tunnel is the dominant root cause of the silent hard-locks. Pre-drive uptime was 33 days; with drive, repeated crashes despite UAS blacklist + mount-on-demand. **Result so far:** 3+ days uptime — the drive looks like the primary contributor; `cpu-epp` remains as belt-and-suspenders thermal protection. See [investigation](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md).
 
 ### 2026-04-22 — `cpu-epp.service` ordering bug fixed
 Was `After=multi-user.target` + `WantedBy=multi-user.target` — queued behind `pve-guests.service`, so the hottest boot window (20+ guests starting on `performance`) preceded EPP application. Now `After=sysinit.target` + `Before=pve-guests.service`.
@@ -159,4 +159,4 @@ Was `After=multi-user.target` + `WantedBy=multi-user.target` — queued behind `
 `60-crash-capture.conf`, softdog `soft_panic=1`, RuntimeWatchdog 15 s. `rasdaemon` installed and enabled. Pure silicon hangs still leave no trace; this catches everything else.
 
 ### 2026-04-21 — `cpu-epp.service` deployed
-Pinned governor=`powersave`, EPP=`balance_power` at boot. Stopped the host idling at ~95 °C with everything pinned at 4.4 GHz. First fix in the [crash-loop incident](../../../investigations/archive/2026-04-21-hubris-crash-loop.md).
+Pinned governor=`powersave`, EPP=`balance_power` at boot. Stopped the host idling at ~95 °C with everything pinned at 4.4 GHz. First fix in the [crash-loop incident](../../sources/investigations/archive/2026-04-21-hubris-crash-loop.md).