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/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