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>

state/system-instructions.json

@@ -0,0 +1 @@
+{"version":"1.0.0","description":"Central process definitions for all agents","processes":{"model-selection":{"description":"Cost-efficient model selection","rules":["Start with lowest capable model","Escalate only when task complexity requires","Agents may request model upgrade from orchestrator","Log model usage for cost analysis"]},"cross-agent-communication":{"description":"How agents interact","flow":"Agent A → Master Orchestrator → Personal Assistant (if escalation needed)","hierarchy":"Personal Assistant → Master Orchestrator → Domain Agents","requirements":["All cross-agent requests routed through master orchestrator","Master validates, routes, and logs all requests","Personal assistant has ultimate escalation authority","No direct agent-to-agent communication"]},"autonomy-enforcement":{"description":"How autonomy levels are applied","default":"conservative","session_override_file":"~/.claude/state/sysadmin/session-autonomy.json","rules":["Master orchestrator enforces autonomy levels","Session overrides apply only for current session","Forbidden actions always blocked regardless of autonomy level"]},"file-management":{"description":"File and directory ownership","state-files":{"system-instructions.json":"master-orchestrator","future-considerations.json":"master-orchestrator","model-policy.json":"master-orchestrator","autonomy-levels.json":"master-orchestrator","session-autonomy.json":"user/CLI"},"directories":{"master-orchestrator":["agents/","state/","skills/","commands/","workflows/"],"linux-sysadmin":["state/sysadmin/","automation/"]},"override_authority":"personal-assistant"},"agent-lifecycle":{"add":["Create agents/<name>.md","Update supervisor hierarchy","Update CLAUDE.md diagram","Update model-policy.json"],"remove":["Remove agents/<name>.md","Update supervisor hierarchy","Update CLAUDE.md diagram","Update model-policy.json","Clean up state"]},"content-principles":{"no-redundancy":"Information lives in one authoritative location","lean-files":"Keep files concise - no verbose examples or unnecessary prose"},"deferral-capture":{"description":"Capture deferrals to future-considerations.json","trigger":"User says 'revisit later' or similar","behavior":"Watch user messages for items worth adding to future-considerations.json - both explicit deferrals and implicit mentions of future work"}}}