feat(protocols): add protocols artifact convention, sys-medic protocol + CLI (WP-0002 T17-T24)

- ADR-003: protocols artifact convention (location, structure, lifecycle) - agents/protocols/README.md: directory-level index and usage guide - agents/protocols/sys-medic/k3s-node-health-assessment.md: full structured k3s node health assessment protocol (8 steps: OS baseline, process hygiene, memory, CPU, disk, network, k3s node state, runtime services) - agent-sys-medic.md: add memory: enabled frontmatter, session-start/close protocols, node-profile memory template extensions, protocol reference in Default Task - cli.py: add protocols command group (list, show); extend memory init to hint protocol commands for agents that have protocols Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2026-03-18 23:48:09 +00:00
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+# Agent Protocols
+
+This directory contains **protocol runbooks** — structured, human-readable procedural documents that kaizen-agentic agents reference during structured assessments or remediation work.
+
+Protocols are distinct from agent prompts:
+- **Agent prompts** (`agents/agent-*.md`) shape AI behaviour
+- **Protocols** (`agents/protocols/<agent>/<slug>.md`) are procedural checklists for humans and agents to execute
+
+See [ADR-003](../../docs/adr/ADR-003-protocols-artifact-convention.md) for the full convention.
+
+## Structure
+
+```
+agents/protocols/
+  <agent-name>/
+    <slug>.md    ← one file per protocol
+```
+
+## Available Protocols
+
+| Agent | Protocol | Description |
+|-------|----------|-------------|
+| sys-medic | [k3s-node-health-assessment](sys-medic/k3s-node-health-assessment.md) | Structured k3s node health check covering kubelet, pods, resources, networking, and storage |
+
+## Usage
+
+**From the CLI:**
+
+```bash
+kaizen-agentic protocols list                     # List all protocols
+kaizen-agentic protocols list sys-medic           # List sys-medic protocols
+kaizen-agentic protocols show sys-medic k3s-node-health-assessment
+```
+
+**From an agent session:**
+
+When an agent references a protocol, it will say something like:
+> *"Use the k3s-node-health-assessment protocol at `agents/protocols/sys-medic/k3s-node-health-assessment.md` for this assessment."*
+
+Protocols can also be read and executed directly without an AI agent.
--- a/agents/protocols/sys-medic/k3s-node-health-assessment.md
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+---
+agent: sys-medic
+slug: k3s-node-health-assessment
+title: k3s Node Health Assessment
+version: 1.0.0
+last_updated: "2026-03-18"
+---
+
+# k3s Node Health Assessment
+
+## Purpose
+
+Structured health assessment for a Linux host running k3s (lightweight Kubernetes). Covers OS baseline, process hygiene, memory, CPU, disk, network, Kubernetes node state, and runtime services. Produces a prioritized findings report with safe next actions.
+
+## Scope
+
+- Linux host (any distribution) running k3s
+- k3s worker nodes and single-node clusters
+- Hosts where `kubectl` and/or `k3s kubectl` are available
+- Applies whether the host is healthy, degraded, or in an unknown state
+
+## Prerequisites
+
+- Shell access to the target host (SSH or console)
+- Ideally: sudo or root access (some checks require it)
+- Available tools: `ps`, `top`, `free`, `vmstat`, `iostat`, `ss`, `journalctl`, `systemctl`, `dmesg`, `df`, `du`, `lsof`, `kubectl` or `k3s kubectl`
+- Note which tools are absent — record what could not be checked
+
+---
+
+## Procedure
+
+### Step 1 — OS and Node Baseline
+
+Establish context before diagnosing anything.
+
+```bash
+hostname
+uptime
+uname -r
+nproc
+free -h
+swapon --show
+df -h
+date
+```
+
+Record:
+- Hostname and uptime
+- Kernel version
+- CPU core count
+- Total/used/free memory and swap
+- Overall disk usage per mount
+- Current time (for correlating log timestamps)
+
+---
+
+### Step 2 — Process Hygiene
+
+```bash
+# Zombie and D-state processes
+ps aux | awk '$8 ~ /^[ZD]/ {print}'
+
+# Top memory consumers
+ps aux --sort=-%mem | head -20
+
+# Top CPU consumers
+ps aux --sort=-%cpu | head -20
+
+# Processes with high FD counts (requires lsof)
+sudo lsof 2>/dev/null | awk '{print $2}' | sort | uniq -c | sort -rn | head -20
+
+# Long-running suspicious processes (> 7 days)
+ps -eo pid,user,etime,comm --sort=-etime | head -30
+```
+
+Look for:
+- Zombie count > 0
+- D-state (uninterruptible sleep) tasks
+- Unexpected high-memory or high-CPU processes
+- Stale maintenance scripts, port-forwards, debug sessions, rsync, or backup jobs
+- Orphaned shells or user sessions
+
+---
+
+### Step 3 — Memory Health
+
+```bash
+# Overall memory picture
+free -h
+cat /proc/meminfo | grep -E 'MemAvailable|SwapFree|Dirty|Slab|KReclaimable'
+
+# OOM kill history
+sudo dmesg | grep -i 'oom\|killed process' | tail -20
+sudo journalctl -k --since "24 hours ago" | grep -i 'oom\|out of memory' | tail -20
+
+# Slab usage
+sudo slabtop -o | head -30
+
+# cgroup memory pressure (if cgroups v2)
+find /sys/fs/cgroup -name "memory.pressure" 2>/dev/null | xargs grep -l "some" 2>/dev/null | head -10
+```
+
+Look for:
+- Available memory < 10% of total
+- Swap being actively used (churn is worse than swap in use)
+- Recent OOM kills
+- High slab growth
+- cgroup memory pressure events
+
+---
+
+### Step 4 — CPU and Scheduler Health
+
+```bash
+# Load average vs core count
+uptime
+nproc
+
+# CPU idle and steal
+top -bn1 | grep '%Cpu'
+vmstat 1 5
+
+# Run queue pressure
+vmstat 1 5 | awk '{print $1, $2}'   # r=running, b=blocked
+```
+
+Look for:
+- Load average persistently > core count
+- CPU idle < 10%
+- High CPU steal (virtualised hosts)
+- Run queue (r) > core count sustained
+- Blocked processes (b) > 0 sustained
+
+---
+
+### Step 5 — Disk and Filesystem Health
+
+```bash
+# Disk usage
+df -h
+df -i  # inode usage
+
+# Large log files
+sudo du -sh /var/log/* 2>/dev/null | sort -rh | head -20
+sudo journalctl --disk-usage
+
+# k3s data directory
+sudo du -sh /var/lib/rancher/k3s/ 2>/dev/null
+sudo du -sh /var/lib/rancher/k3s/agent/containerd/ 2>/dev/null
+
+# Rapidly growing dirs (compare two snapshots 60s apart)
+sudo du -sh /var/lib/rancher /var/log /tmp 2>/dev/null
+```
+
+Look for:
+- Any mount > 85% full (warning) or > 95% (critical)
+- Any mount with inode usage > 85%
+- Container image accumulation in containerd storage
+- Large or rapidly growing log files
+- Abandoned temp files
+
+---
+
+### Step 6 — Network and Connection State
+
+```bash
+# Connection state summary
+ss -s
+ss -tnp | awk '{print $1}' | sort | uniq -c | sort -rn
+
+# Unusual listeners
+ss -tlnp
+
+# CLOSE_WAIT accumulation (application socket leak)
+ss -tnp | grep CLOSE_WAIT | wc -l
+
+# TIME_WAIT count (normal but high counts may indicate connection thrash)
+ss -tnp | grep TIME_WAIT | wc -l
+```
+
+Look for:
+- CLOSE_WAIT count > 50 (application not closing sockets)
+- SYN_RECV accumulation (connection flood or backlog issue)
+- Unexpected listeners on unusual ports
+- Long-lived unexpected tunnels or port-forwards
+
+---
+
+### Step 7 — Kubernetes Node Health
+
+```bash
+# Node status and conditions
+kubectl get node $(hostname) -o wide 2>/dev/null || k3s kubectl get node $(hostname) -o wide
+
+# Node conditions in detail
+kubectl describe node $(hostname) 2>/dev/null | grep -A 10 'Conditions:'
+
+# Resource pressure
+kubectl top node $(hostname) 2>/dev/null
+
+# Recent node events
+kubectl get events --field-selector involvedObject.name=$(hostname) --sort-by='.lastTimestamp' 2>/dev/null | tail -20
+
+# Top pods by resource use
+kubectl top pods --all-namespaces --sort-by=memory 2>/dev/null | head -20
+
+# Restarting pods on this node
+kubectl get pods --all-namespaces --field-selector spec.nodeName=$(hostname) 2>/dev/null | awk '$5 > 5 {print}'
+```
+
+Look for:
+- Node Ready=False or Unknown
+- MemoryPressure, DiskPressure, PIDPressure, or NetworkUnavailable = True
+- Pods with high restart counts (> 5)
+- CrashLoopBackOff workloads
+- Evicted pods (indicates past resource pressure)
+
+---
+
+### Step 8 — k3s Runtime and Control Services
+
+```bash
+# k3s service status
+sudo systemctl status k3s 2>/dev/null || sudo systemctl status k3s-agent
+
+# k3s recent logs (last 100 lines)
+sudo journalctl -u k3s --since "1 hour ago" -n 100 2>/dev/null || \
+sudo journalctl -u k3s-agent --since "1 hour ago" -n 100
+
+# containerd status (k3s embedded)
+sudo systemctl status containerd 2>/dev/null
+
+# CNI / flannel if applicable
+sudo systemctl status flanneld 2>/dev/null
+sudo ip addr show flannel.1 2>/dev/null
+```
+
+Look for:
+- k3s service not running or in failed state
+- Repeated restart entries in k3s logs
+- PLEG errors, image GC failures, sandbox creation failures
+- cgroup-related errors
+- API server timeout messages (on worker nodes: etcd or API server unreachable)
+
+---
+
+## Interpretation
+
+| Signal | Normal | Warning | Critical |
+|--------|--------|---------|----------|
+| Load average | ≤ core count | 1–2× core count | > 2× sustained |
+| Memory available | > 20% | 10–20% | < 10% |
+| Disk usage | < 75% | 75–90% | > 90% |
+| Inode usage | < 75% | 75–90% | > 90% |
+| Zombie count | 0 | 1–5 | > 5 or climbing |
+| OOM kills (24h) | 0 | 1–2 | > 2 or recent |
+| Pod restarts | < 3 | 3–10 | > 10 or CrashLoop |
+| CLOSE_WAIT | < 10 | 10–50 | > 50 |
+| Node Ready | True | — | False / Unknown |
+
+Confidence in findings:
+- **High** — direct evidence (OOM kill log, node condition set, error in service log)
+- **Medium** — indirect evidence (high memory use without OOM, rising load with no clear cause)
+- **Low** — circumstantial (aging process without other indicators)
+
+---
+
+## Remediation
+
+### High memory pressure
+
+1. Identify top consumers: `ps aux --sort=-%mem | head -20`
+2. Check for OOM history: `dmesg | grep -i oom`
+3. If a workload is leaking: restart the specific pod (not the node)
+4. If slab is high: check for inode-heavy workloads or NFS mounts
+5. Do not drop caches unless explicitly justified — Linux reclaims page cache automatically
+
+### Disk pressure
+
+1. Find largest directories: `du -sh /var/lib/rancher/k3s/agent/containerd/io.containerd.snapshotter.v1.overlayfs/snapshots/* | sort -rh | head -20`
+2. Prune unused container images: `k3s crictl rmi --prune` (safe — only removes unused images)
+3. Clear old journal logs: `sudo journalctl --vacuum-size=500M`
+4. Identify log-bloating pods and fix their logging config
+
+### k3s service failing
+
+1. Check service status: `sudo systemctl status k3s`
+2. Check logs: `sudo journalctl -u k3s -n 200`
+3. Common causes: etcd data corruption (single-node), API server unreachable (worker), disk full, cert expiry
+4. Do not restart k3s without understanding the cause — a restart may mask the issue
+
+### High pod restart count
+
+1. Check logs: `kubectl logs <pod> --previous`
+2. Check events: `kubectl describe pod <pod>`
+3. Distinguish OOMKilled (memory limit) from CrashLoop (application error) from Liveness probe failure
+
+---
+
+## Notes
+
+- This protocol was adapted from the sys-medic agent's structured assessment areas and the sys-medic repo's companion protocol document.
+- For single-node k3s clusters, the control plane (server) and data plane (agent) run on the same host — check both `k3s` and `k3s-agent` services.
+- On hosts without `kubectl` in PATH, use `k3s kubectl` as a drop-in replacement.
+- Protocol version history is tracked via the `version` frontmatter field. Update on significant structural changes.