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/autonomy-levels.json

@@ -0,0 +1 @@
+{"version":"1.0.0","description":"Shared autonomy level definitions for all agents","levels":{"conservative":{"description":"Confirm all write operations","behavior":{"read_operations":"auto-execute","write_operations":"require confirmation","destructive_operations":"require confirmation"},"suitable_for":["initial setup","unfamiliar systems","production environments"]},"moderate":{"description":"Auto-execute routine maintenance, confirm installs/removals","behavior":{"read_operations":"auto-execute","routine_maintenance":"auto-execute","package_changes":"require confirmation","destructive_operations":"require confirmation"},"suitable_for":["trusted development environments","routine maintenance"]},"trusted":{"description":"Auto-execute most operations, confirm only destructive","behavior":{"read_operations":"auto-execute","write_operations":"auto-execute","package_changes":"auto-execute","destructive_operations":"require confirmation"},"suitable_for":["well-known environments","time-sensitive operations"]}},"agent_defaults":{"linux-sysadmin":"conservative","k8s-orchestrator":"conservative","k8s-diagnostician":"conservative","argocd-operator":"conservative","prometheus-analyst":"conservative","git-operator":"conservative"},"session_override":{"file":"~/.claude/state/sysadmin/session-autonomy.json","applies_to":"current session only","reset_on":"session end"}}

state/kb.json

@@ -0,0 +1 @@
+{"infra":{"cluster":"k0s","nodes":3,"arch":"arm64"},"svc":{"gitops":"argocd","mon":"prometheus","alerts":"alertmanager"},"net":{},"hw":{"pi5_8gb":2,"pi3_1gb":1}}

state/model-policy.json

@@ -0,0 +1,68 @@
+{
+  "version": "1.0.0",
+  "description": "Cost-efficient model selection policy",
+  "models": {
+    "opus": {
+      "use_cases": [
+        "Complex reasoning and analysis",
+        "Cross-agent coordination",
+        "Policy enforcement and validation",
+        "Architectural decisions",
+        "Ambiguous or nuanced tasks"
+      ],
+      "agents": [
+        "personal-assistant",
+        "master-orchestrator",
+        "k8s-orchestrator",
+        "programmer-orchestrator"
+      ]
+    },
+    "sonnet": {
+      "use_cases": [
+        "Standard operations",
+        "Well-defined tasks",
+        "Routine automation",
+        "Code generation and modification",
+        "Troubleshooting with clear symptoms"
+      ],
+      "agents": [
+        "linux-sysadmin",
+        "k8s-diagnostician",
+        "argocd-operator",
+        "prometheus-analyst",
+        "git-operator",
+        "code-planner",
+        "code-implementer",
+        "code-reviewer"
+      ]
+    },
+    "haiku": {
+      "use_cases": [
+        "Simple queries",
+        "Status checks",
+        "Log parsing",
+        "Data extraction",
+        "Formatting and summarization"
+      ],
+      "agents": [],
+      "delegation_note": "Any agent can delegate simple subtasks to Haiku for cost efficiency"
+    }
+  },
+  "escalation_rules": [
+    {
+      "from": "haiku",
+      "to": "sonnet",
+      "triggers": ["task_too_complex", "context_insufficient", "reasoning_required"]
+    },
+    {
+      "from": "sonnet",
+      "to": "opus",
+      "triggers": ["cross_agent_coordination", "policy_decision", "complex_analysis"]
+    }
+  ],
+  "cost_optimization": {
+    "default_start": "lowest_capable",
+    "log_usage": true,
+    "review_frequency": "weekly"
+  }
+}

state/personal-assistant-preferences.json

@@ -1,7 +1 @@
-{
-  "version": "1.0",
-  "description": "Persistent PA configuration",
-  "context_gathering": {
-    "default_level": "moderate"
-  }
-}
+{"version":"1.0","description":"Persistent PA configuration","context_gathering":{"default_level":"moderate"}}

state/personal-assistant/general-instructions.json

@@ -1,5 +1,12 @@
 {
   "version": "1.0",
   "description": "User instructions optimized for agent consumption",
-  "items": []
+  "items": [
+    {
+      "id": "a1b2c3d4-5678-90ab-cdef-111111111111",
+      "instruction": "Delegate technical tasks to specialized agents. Use skills and slash commands for quick technical checks.",
+      "status": "active",
+      "added": "2025-01-21"
+    }
+  ]
 }

state/personal-assistant/history/index.json

@@ -0,0 +1,131 @@
+{
+  "version": "1.0",
+  "sessions": [
+    {
+      "id": "2025-12-29_10-36-32",
+      "started": "2025-12-29T10:36:32-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_10-38-46",
+      "started": "2025-12-29T10:38:46-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_10-59-33",
+      "started": "2025-12-29T10:59:33-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-10-38",
+      "started": "2025-12-29T11:10:38-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-20-09",
+      "started": "2025-12-29T11:20:09-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-20-12",
+      "started": "2025-12-29T11:20:12-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-20-17",
+      "started": "2025-12-29T11:20:17-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-20-25",
+      "started": "2025-12-29T11:20:25-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-20-49",
+      "started": "2025-12-29T11:20:49-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-25-40",
+      "started": "2025-12-29T11:25:40-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-25-44",
+      "started": "2025-12-29T11:25:44-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-26-31",
+      "started": "2025-12-29T11:26:31-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-26-33",
+      "started": "2025-12-29T11:26:33-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-28-05",
+      "started": "2025-12-29T11:28:05-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-28-06",
+      "started": "2025-12-29T11:28:06-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_11-47-07",
+      "started": "2025-12-29T11:47:07-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_12-31-06",
+      "started": "2025-12-29T12:31:06-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    },
+    {
+      "id": "2025-12-29_12-31-10",
+      "started": "2025-12-29T12:31:10-08:00",
+      "ended": null,
+      "summarized": false,
+      "topics": []
+    }
+  ]
+}

state/personal-assistant/kb.json

@@ -0,0 +1 @@
+{}

state/personal-assistant/memory/decisions.json

@@ -0,0 +1,5 @@
+{
+  "version": "1.0",
+  "description": "Decisions made with rationale",
+  "items": []
+}

state/personal-assistant/memory/facts.json

@@ -0,0 +1,5 @@
+{
+  "version": "1.0",
+  "description": "Factual knowledge about the environment",
+  "items": []
+}

state/personal-assistant/memory/meta.json

@@ -0,0 +1,11 @@
+{
+  "version": "1.0",
+  "last_summarized": null,
+  "total_sessions": 0,
+  "total_items": {
+    "decisions": 0,
+    "preferences": 0,
+    "projects": 0,
+    "facts": 0
+  }
+}

state/personal-assistant/memory/preferences.json

@@ -0,0 +1,5 @@
+{
+  "version": "1.0",
+  "description": "User preferences learned over time",
+  "items": []
+}

state/personal-assistant/memory/projects.json

@@ -0,0 +1,5 @@
+{
+  "version": "1.0",
+  "description": "Active and recent project context",
+  "items": []
+}

state/personal-assistant/session-context.json

@@ -1,6 +1 @@
-{
-  "version": "1.0",
-  "current_context_level": null,
-  "set_at": null,
-  "set_by": null
-}
+{"version":"1.0","current_context_level":null,"set_at":null,"set_by":null}

state/programmer/preferences.json

@@ -0,0 +1,5 @@
+{
+  "style": {},
+  "patterns": {},
+  "languages": {}
+}

state/programmer/session-autonomy.json

@@ -0,0 +1,4 @@
+{
+  "level": "conservative",
+  "overrides": {}
+}

state/sysadmin/session-autonomy.json

@@ -0,0 +1 @@
+{"version":"1.0.0","description":"Per-session autonomy overrides for linux-sysadmin agent","current_level":"conservative","session_start":null,"overrides":{},"notes":"This file is modified by user/CLI to adjust autonomy during a session"}

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"}}}