Implement programmer agent system and consolidate agent infrastructure

Programmer Agent System:
- Add programmer-orchestrator (Opus) for workflow coordination
- Add code-planner (Sonnet) for design and planning
- Add code-implementer (Sonnet) for writing code
- Add code-reviewer (Sonnet) for quality review
- Add /programmer command and project registration skill
- Add state files for preferences and project context

Agent Infrastructure:
- Add master-orchestrator and linux-sysadmin agents
- Restructure skills to use SKILL.md subdirectory format
- Convert workflows from markdown to YAML format
- Add commands for k8s and sysadmin domains
- Add shared state files (model-policy, autonomy-levels, system-instructions)
- Add PA memory system (decisions, preferences, projects, facts)

Cleanup:
- Remove deprecated markdown skills and workflows
- Remove crontab example (moved to workflows)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

workflows/deploy/deploy-app.md

@@ -1,97 +0,0 @@
-# Deploy Application Workflow
-
-A simple workflow for deploying new applications or updating existing ones.
-
-## When to use
-
-Use this workflow when:
-- Deploying a new application to the cluster
-- Updating an existing application's configuration
-- Rolling out a new version of an application
-
-## Steps
-
-### 1. Gather Requirements
-
-Ask the user for:
-- Application name
-- Container image and tag
-- Namespace (default: `default`)
-- Resource requirements (CPU/memory limits)
-- Exposed ports
-- Any special requirements (tolerations for Pi 3, etc.)
-
-### 2. Check Existing State
-
-Delegate to **argocd-operator** (haiku):
-- Check if application already exists in ArgoCD
-- If exists, get current status and version
-
-Delegate to **k8s-diagnostician** (haiku):
-- If exists, check current pod status
-- Check namespace exists
-
-### 3. Create/Update Manifests
-
-Delegate to **git-operator** (sonnet):
-- Create or update deployment manifest
-- Create or update service manifest (if ports exposed)
-- Create or update kustomization.yaml
-- Include appropriate resource limits for Pi cluster:
-  ```yaml
-  resources:
-    requests:
-      memory: "64Mi"
-      cpu: "50m"
-    limits:
-      memory: "128Mi"
-      cpu: "200m"
-  ```
-- If targeting Pi 3, add tolerations:
-  ```yaml
-  tolerations:
-    - key: "node-type"
-      operator: "Equal"
-      value: "pi3"
-      effect: "NoSchedule"
-  ```
-
-### 4. Commit Changes
-
-Delegate to **git-operator** (sonnet):
-- Create feature branch: `deploy/<app-name>`
-- Commit with message: `feat: deploy <app-name>`
-- Push branch to origin
-- Create pull request
-
-**[CONFIRM]** User must approve the PR creation.
-
-### 5. Sync Application
-
-After PR is merged:
-
-Delegate to **argocd-operator** (sonnet):
-- Create ArgoCD application if new
-- Trigger sync for the application
-- Wait for sync to complete
-
-**[CONFIRM]** User must approve the sync operation.
-
-### 6. Verify Deployment
-
-Delegate to **k8s-diagnostician** (haiku):
-- Check pods are running
-- Check no restart loops
-- Verify resource usage is within limits
-
-Report final status to user.
-
-## Rollback
-
-If deployment fails:
-
-Delegate to **argocd-operator**:
-- Check application history
-- Propose rollback to previous version
-
-**[CONFIRM]** User must approve rollback.

workflows/deploy/deploy-app.yaml

@@ -0,0 +1,118 @@
+name: deploy-app
+description: Deploy new application or update existing one
+version: "1.0"
+
+trigger:
+  - manual: true
+
+inputs:
+  app_name:
+    description: Application name
+    required: true
+  image:
+    description: Container image and tag
+    required: true
+  namespace:
+    description: Target namespace
+    default: "default"
+  ports:
+    description: Exposed ports (comma-separated)
+    required: false
+  pi3_compatible:
+    description: Add tolerations for Pi 3 node
+    default: false
+
+defaults:
+  model: sonnet
+
+steps:
+  - name: check-existing
+    description: Check if application already exists
+    parallel:
+      - agent: argocd-operator
+        model: haiku
+        task: |
+          Check if application '{{ inputs.app_name }}' exists in ArgoCD.
+          If exists, get current status, version, and sync state.
+        output: argocd_status
+
+      - agent: k8s-diagnostician
+        model: haiku
+        task: |
+          Check if namespace '{{ inputs.namespace }}' exists.
+          If app exists, check current pod status for '{{ inputs.app_name }}'.
+        output: k8s_status
+
+  - name: create-manifests
+    agent: git-operator
+    model: sonnet
+    task: |
+      Create or update Kubernetes manifests for '{{ inputs.app_name }}':
+
+      1. Deployment manifest with:
+         - Image: {{ inputs.image }}
+         - Namespace: {{ inputs.namespace }}
+         - Resource limits (Pi-optimized):
+           requests: {memory: "64Mi", cpu: "50m"}
+           limits: {memory: "128Mi", cpu: "200m"}
+         {% if inputs.pi3_compatible %}
+         - Tolerations for Pi 3 node
+         {% endif %}
+
+      2. Service manifest (if ports specified: {{ inputs.ports }})
+
+      3. Kustomization.yaml
+
+      Existing state:
+      - ArgoCD: {{ steps.check-existing.argocd_status }}
+      - K8s: {{ steps.check-existing.k8s_status }}
+    output: manifests
+    confirm: true
+
+  - name: commit-changes
+    agent: git-operator
+    model: sonnet
+    task: |
+      Commit the manifests to GitOps repository:
+      1. Create feature branch: deploy/{{ inputs.app_name }}
+      2. Commit with message: feat: deploy {{ inputs.app_name }}
+      3. Push branch to origin
+      4. Create pull request
+    output: pr_url
+    confirm: true
+
+  - name: sync-application
+    agent: argocd-operator
+    model: sonnet
+    task: |
+      After PR is merged:
+      1. Create ArgoCD application if new
+      2. Trigger sync for '{{ inputs.app_name }}'
+      3. Wait for sync to complete
+      4. Report sync result
+    output: sync_result
+    confirm: true
+    depends_on_user: "PR must be merged before continuing"
+
+  - name: verify-deployment
+    agent: k8s-diagnostician
+    model: haiku
+    task: |
+      Verify deployment of '{{ inputs.app_name }}':
+      - Check pods are running
+      - Check no restart loops
+      - Verify resource usage within limits
+      Report final deployment status.
+    output: verification
+
+on_failure:
+  - name: propose-rollback
+    agent: argocd-operator
+    task: |
+      Deployment failed. Check application history and propose rollback.
+    confirm: true
+
+outputs:
+  - pr_url
+  - sync_result
+  - verification

workflows/health/cluster-daily-summary.yaml

@@ -0,0 +1,40 @@
+name: cluster-daily-summary
+description: Lightweight daily cluster status summary
+version: "1.0"
+
+trigger:
+  - schedule: "0 8 * * *"  # daily at 8am
+  - manual: true
+
+defaults:
+  model: haiku
+
+steps:
+  - name: quick-status
+    agent: k8s-diagnostician
+    model: haiku
+    task: |
+      Generate a quick daily cluster status:
+
+      1. Node overview:
+         - kubectl get nodes -o wide
+         - Any nodes not Ready?
+
+      2. Pod health:
+         - Count of running vs non-running pods
+         - Any pods in CrashLoopBackOff or Error?
+
+      3. ArgoCD sync status:
+         - argocd app list (if available)
+         - Any apps OutOfSync?
+
+      4. Recent events:
+         - kubectl get events --sort-by='.lastTimestamp' -A | tail -10
+         - Any Warning events in last 24h?
+
+      Format as a brief daily digest suitable for quick review.
+      Keep it concise - this is a summary, not a deep dive.
+    output: daily_summary
+
+outputs:
+  - daily_summary

workflows/sysadmin/health-check.yaml

@@ -0,0 +1,50 @@
+name: sysadmin-health-check
+description: Scheduled health check for Arch Linux workstation
+version: "1.0.0"
+
+trigger:
+  schedule:
+    cron: "0 9 * * *"  # Daily at 9 AM
+  manual: true
+
+agent: linux-sysadmin
+model: haiku  # Use haiku for cost efficiency
+
+steps:
+  - name: collect-metrics
+    description: Gather system metrics
+    commands:
+      - df -h
+      - free -h
+      - uptime
+      - top -bn1 | head -20
+
+  - name: check-packages
+    description: Check package status
+    commands:
+      - checkupdates 2>/dev/null || echo "No updates"
+      - yay -Qua 2>/dev/null || echo "No AUR updates"
+      - pacman -Qtdq 2>/dev/null || echo "No orphans"
+
+  - name: check-services
+    description: Check systemd services
+    commands:
+      - systemctl --failed --no-pager
+
+  - name: check-logs
+    description: Review recent errors
+    commands:
+      - journalctl -p err --since "24 hours ago" -n 10 --no-pager
+
+  - name: generate-report
+    description: Create health summary
+    action: summarize
+    format: markdown
+
+output:
+  file: ~/.claude/logs/health-reports/$(date +%Y-%m-%d).md
+  notify:
+    on_warning: true
+    on_critical: true
+
+autonomy: read-only  # No confirmation needed for read operations

workflows/sysadmin/system-update.yaml

@@ -0,0 +1,83 @@
+name: sysadmin-system-update
+description: Manual system update workflow for Arch Linux
+version: "1.0.0"
+
+trigger:
+  manual: true
+  command: /update
+
+agent: linux-sysadmin
+model: sonnet  # Use sonnet for update decisions
+
+parameters:
+  - name: scope
+    type: choice
+    options: [full, pacman, aur, brew]
+    default: full
+    description: Which package managers to update
+
+  - name: dry_run
+    type: boolean
+    default: false
+    description: Show updates without installing
+
+steps:
+  - name: pre-flight
+    description: Pre-update checks
+    commands:
+      - df -h /  # Check disk space
+      - pacman -Qi linux | grep Version  # Current kernel version
+    fail_on_error: true
+
+  - name: check-updates
+    description: List available updates
+    commands:
+      - checkupdates
+      - yay -Qua
+      - brew outdated
+    condition: "{{ not dry_run }}"
+
+  - name: confirm-updates
+    description: Get user confirmation
+    action: confirm
+    message: "Proceed with {{ scope }} update?"
+    skip_if: "{{ autonomy == 'trusted' }}"
+
+  - name: update-pacman
+    description: Update pacman packages
+    commands:
+      - pacman -Syu --noconfirm
+    condition: "{{ scope in ['full', 'pacman'] }}"
+    requires_confirmation: true
+
+  - name: update-aur
+    description: Update AUR packages
+    commands:
+      - yay -Sua --noconfirm
+    condition: "{{ scope in ['full', 'aur'] }}"
+    requires_confirmation: true
+
+  - name: update-brew
+    description: Update Homebrew packages
+    commands:
+      - brew upgrade
+    condition: "{{ scope in ['full', 'brew'] }}"
+    requires_confirmation: true
+
+  - name: post-update
+    description: Post-update checks
+    commands:
+      - find /etc -name "*.pacnew" 2>/dev/null
+      - pacman -Qi linux | grep Version  # Check if kernel updated
+    action: summarize
+
+  - name: reboot-check
+    description: Check if reboot needed
+    action: notify
+    message: "Kernel updated. Reboot recommended."
+    condition: "{{ kernel_updated }}"
+
+output:
+  log: ~/.claude/logs/updates/$(date +%Y-%m-%d_%H%M).log
+
+autonomy: conservative  # Always confirm update operations

workflows/validate-agent-format.yaml

@@ -0,0 +1,62 @@
+name: validate-agent-format
+description: Validate YAML frontmatter in all agent definition files
+trigger:
+  - manual
+
+inputs: {}
+
+steps:
+  - name: scan-agent-files
+    description: Find all agent definition files
+    command: ls -1 ~/.claude/agents/*.md
+
+  - name: validate-frontmatter
+    description: Check each agent file for required YAML frontmatter
+    for_each: "{{ steps.scan-agent-files.output }}"
+    validation:
+      - name: has-frontmatter
+        check: "File starts with '---' delimiter"
+        required: true
+
+      - name: has-name-field
+        check: "YAML contains 'name:' field"
+        required: true
+
+      - name: has-description-field
+        check: "YAML contains 'description:' field"
+        required: true
+
+      - name: has-model-field
+        check: "YAML contains 'model:' field"
+        required: true
+
+      - name: has-tools-field
+        check: "YAML contains 'tools:' field"
+        required: true
+
+      - name: valid-model-value
+        check: "model value is one of: haiku, sonnet, opus"
+        required: true
+
+  - name: report-results
+    description: Generate validation report
+    output:
+      format: table
+      columns:
+        - file
+        - has_frontmatter
+        - has_name
+        - has_description
+        - has_model
+        - has_tools
+        - valid_model
+        - status
+
+success_criteria:
+  - all_files_have_frontmatter: true
+  - all_required_fields_present: true
+  - all_model_values_valid: true
+
+on_failure:
+  - report: List files with missing or invalid frontmatter
+  - suggest: Provide exact frontmatter template for each failing file