Fix Issue #1428: Deny bash permission for Prometheus agent

- Change PROMETHEUS_PERMISSION bash from 'allow' to 'deny' to prevent unrestricted bash execution
- Prometheus is a read-only planner and should not execute bash commands
- The prometheus-md-only hook provides additional blocking as backup

src/plugin-handlers/AGENTS.md

@@ -0,0 +1,96 @@
+**Generated:** 2026-02-08T16:45:00+09:00
+**Commit:** f2b7b759
+**Branch:** dev
+
+## OVERVIEW
+
+Plugin component loading and configuration orchestration. 500+ lines of config merging, migration, and component discovery for Claude Code compatibility.
+
+## STRUCTURE
+```
+plugin-handlers/
+├── config-handler.ts       # Main config orchestrator (563 lines) - agent/skill/command loading
+├── config-handler.test.ts  # Config handler tests (34426 lines)
+├── plan-model-inheritance.ts # Plan agent model inheritance logic (657 lines)
+├── plan-model-inheritance.test.ts # Inheritance tests (3696 lines)
+└── index.ts               # Barrel export
+```
+
+## CORE FUNCTIONS
+
+**Config Handler (`createConfigHandler`):**
+- Loads all plugin components (agents, skills, commands, MCPs)
+- Applies permission migrations for compatibility
+- Merges user/project/global configurations
+- Handles Claude Code plugin integration
+
+**Plan Model Inheritance:**
+- Demotes plan agent to prometheus when planner enabled
+- Preserves user overrides during migration
+- Handles model/variant inheritance from categories
+
+## LOADING PHASES
+
+1. **Plugin Discovery**: Load Claude Code plugins with timeout protection
+2. **Component Loading**: Parallel loading of agents, skills, commands
+3. **Config Merging**: User → Project → Global → Defaults
+4. **Migration**: Legacy config format compatibility
+5. **Permission Application**: Tool access control per agent
+
+## KEY FEATURES
+
+**Parallel Loading:**
+- Concurrent discovery of user/project/global components
+- Timeout protection for plugin loading (default: 10s)
+- Error isolation (failed plugins don't break others)
+
+**Migration Support:**
+- Agent name mapping (old → new names)
+- Permission format conversion
+- Config structure updates
+
+**Claude Code Integration:**
+- Plugin component loading
+- MCP server discovery
+- Agent/skill/command compatibility
+
+## CONFIGURATION FLOW
+
+```
+User Config → Migration → Merging → Validation → Agent Creation → Permission Application
+```
+
+## TESTING COVERAGE
+
+- **Config Handler**: 34426 lines of tests
+- **Plan Inheritance**: 3696 lines of tests
+- **Migration Logic**: Legacy compatibility verification
+- **Parallel Loading**: Timeout and error handling
+
+## USAGE PATTERNS
+
+**Config Handler Creation:**
+```typescript
+const handler = createConfigHandler({
+  ctx: { directory: projectDir },
+  pluginConfig: userConfig,
+  modelCacheState: cache
+});
+```
+
+**Plan Demotion:**
+```typescript
+const demotedPlan = buildPlanDemoteConfig(
+  prometheusConfig,
+  userPlanOverrides
+);
+```
+
+**Component Loading:**
+```typescript
+const [agents, skills, commands] = await Promise.all([
+  loadUserAgents(),
+  loadProjectSkills(),
+  loadGlobalCommands()
+]);
+```