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/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]
+```