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>

commands/sysadmin/autonomy.md

@@ -0,0 +1,58 @@
+---
+name: autonomy
+description: View or change session autonomy level
+aliases: [auto]
+modifies: state:sysadmin/session-autonomy
+---
+
+# /autonomy Command
+
+View or change the session autonomy level for agent operations.
+
+## Usage
+
+```
+/autonomy              # Show current autonomy level
+/autonomy <level>      # Set autonomy level for this session
+/autonomy list         # Show all available levels
+```
+
+## Available Levels
+
+| Level | Description | Use When |
+|-------|-------------|----------|
+| **conservative** | Confirm all write operations | Initial setup, unfamiliar systems, production |
+| **moderate** | Auto-execute routine maintenance, confirm installs | Trusted dev environments, routine maintenance |
+| **trusted** | Auto-execute most operations, confirm only destructive | Well-known environments, time-sensitive ops |
+
+## Examples
+
+```bash
+# Check current level
+/autonomy
+# Output: Current autonomy level: conservative
+
+# Set to moderate for this session
+/autonomy moderate
+# Output: Session autonomy set to: moderate
+
+# List all levels with details
+/autonomy list
+```
+
+## State File
+
+Session autonomy is stored in:
+`~/.claude/state/sysadmin/session-autonomy.json`
+
+Changes only apply to the current session and reset when the session ends.
+
+## What It Does
+
+1. **View**: Reads `session-autonomy.json` and displays current level
+2. **Set**: Updates `current_level` in `session-autonomy.json`
+3. **List**: Displays all levels from `autonomy-levels.json` with descriptions
+
+## Autonomy
+
+This command modifies the session state file. The change takes effect immediately for all subsequent agent operations in this session.

commands/sysadmin/health.md

@@ -0,0 +1,58 @@
+---
+name: health
+description: Run system health check
+aliases: [syshealth, check]
+invokes: skill:sysadmin-health
+---
+
+# /health Command
+
+Runs a comprehensive health check on the Arch Linux workstation.
+
+## Usage
+
+```
+/health
+/health --quick    # Skip package checks (faster)
+/health --full     # Include all checks plus security audit
+```
+
+## What It Does
+
+1. Invokes the `sysadmin-health` skill
+2. Collects system metrics (disk, memory, CPU, swap)
+3. Checks for pending updates and package issues
+4. Reviews failed services and recent errors
+5. Reports overall system health status
+
+## Example Output
+
+```
+System Health Report
+═══════════════════════════════════════
+Status: ⚠️ WARNING
+
+Disk Usage:
+  / : 65% (120G/180G)
+  /home : 82% (450G/550G) ⚠️
+
+Memory: 8.2G / 32G (25%)
+Swap: 0B / 8G
+
+Pending Updates: 12 packages
+Failed Services: 1 (bluetooth.service)
+
+Recent Errors: 3 in last 24h
+  - nvidia-persistenced: initialization error
+  - cups: connection refused
+  - bluetooth: adapter not found
+
+Recommended Actions:
+  1. Clean /home (above 80% threshold)
+  2. Fix bluetooth.service: systemctl restart bluetooth
+  3. Run system update: pacman -Syu
+```
+
+## Autonomy
+
+This command is read-only and runs without confirmation.

commands/sysadmin/update.md

@@ -0,0 +1,72 @@
+---
+name: update
+description: Run system package updates
+aliases: [upgrade, sysupdate]
+invokes: workflow:sysadmin/system-update
+---
+
+# /update Command
+
+Runs system package updates on the Arch Linux workstation.
+
+## Usage
+
+```
+/update              # Full update (pacman + AUR + homebrew)
+/update --pacman     # Only pacman packages
+/update --aur        # Only AUR packages
+/update --brew       # Only homebrew packages
+/update --dry-run    # Show what would be updated without installing
+```
+
+## Update Process
+
+### 1. Pre-flight Checks
+- Check available disk space
+- Check for conflicting packages
+- Verify mirror connectivity
+
+### 2. Update Sequence
+```
+pacman -Syu          # System packages first
+yay -Sua             # AUR packages second
+brew upgrade         # Homebrew packages last
+```
+
+### 3. Post-update
+- Check for .pacnew files
+- Report any failed updates
+- Suggest reboot if kernel updated
+
+## Autonomy
+
+This command requires confirmation before executing updates.
+
+Default autonomy level: **conservative** (confirm all changes)
+
+With `--yes` flag or elevated autonomy:
+- Moderate: Auto-execute routine updates, confirm major version changes
+- Trusted: Auto-execute all updates, confirm only kernel changes
+
+## Example Session
+
+```
+> /update
+
+Checking for updates...
+
+Pacman Updates (15 packages):
+  linux 6.7.1 -> 6.7.2 ⚠️ KERNEL
+  firefox 121.0 -> 122.0
+  ... (13 more)
+
+AUR Updates (3 packages):
+  yay 12.3.1 -> 12.3.2
+  ...
+
+Homebrew Updates (2 packages):
+  node 21.5.0 -> 21.6.0
+  ...
+
+Proceed with updates? [y/N]
+```