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.