P0-P8: Full V1.0.0 Alpha implementation + audit reports

Implements 123 tasks across 9 phases (T-001..T-809) totaling 146 source files.

Monorepo (P0):
- 7-package Bun + Turborepo + TypeScript monorepo
- dependency-cruiser enforcing 7 forbidden edges + 5 deep-import rules

Contracts (P0):
- 16 type files (ids/error/event/runtime/ipc/task/worker-result/tool/artifact/evidence/project/provider/permission/ui/capability/platform)

Storage & Events (P1):
- DatabaseManager + MigrationRunner (19 tables, 22 indexes, 5 schema_meta seeds)
- 16 repositories (Repository<T,I,U> pattern, INV-1 status columns via EventStore.project only)
- EventSchemaRegistry (54 durable + 7 ephemeral), EventStore, EventBus, EventIngestor
- Project/Session/Artifact/Evidence stores + 8-step Recovery

Tools & Permission (P2):
- PathClassifier (8 categories), CommandRiskAnalyzer (10 categories), SecretRedactor
- PermissionEngine 6-layer evaluation (capability→profile→task_scope→risk→credential→user_prompt)
- ToolRegistry with 20+ tools across fs/shell/git/project/artifact/context/permission/doctor
- CapabilityManifestValidator + CapabilityRegistry

LLM & Context (P3):
- ModelConfigLoader, CapabilityMatrix, AnthropicCanonicalConverter
- AnthropicAdapter + OpenAICompatibleAdapter
- ProviderManager facade
- PromptLayerLoader (L0/L1/L3/L5), CompactionPolicy, ContextAssembler

Worker IPC & Scheduler (P4):
- WorkerProtocol (NDJSON), WorkerProcess (exit codes 0-5), WorkerManager (spawn/handshake)
- WorkerRuntime (INV-3: IPC only, no direct fs/shell/SQLite)
- 5 worker roles (Executor/Reviewer/Debugger/Compactor/ExperienceMiner)
- TaskGraph, WavePlanner, RetryPlanner, AgentMonitor, WorkspaceManager
- Scheduler (state machine), 8-step Recovery

C++ Toolchain (P5):
- DiagnosticParser, CppProjectDetector, CMakeConfigurator, CppBuilder
- CppTestRunner, CppcheckRunner, ClangdClient
- CppToolRegistrar + capability manifest

Projection & TUI (P6):
- ProjectionStore (hydrate/apply/snapshot/subscribe)
- TuiApp + 8 components (Session/Task/Agent/Tool/Diff/Evidence/Permission/Blocker/Hud)
- ProjectionClient in-process ref

Agents & Knowledge (P7):
- MainAgent, ArchitectureDesigner
- DebugKnowledgeStore + LearnedMemoryStore (single-writer, outbox model)
- Role integration wiring

CLI & Doctor & Release (P8):
- Logger + DeveloperLogEncryptor (AES-256-GCM)
- DoctorService (self_bootstrap first)
- RuntimeApp + ServiceRegistry
- 11 CLI commands: run/init/doctor/provider/resume/compact/history/session/restore/e2e/release
- CliEntrypoint + air<TODO>

Audit (in AirPlan/docs/):
- Deepseek开发阶段审计.md (97 findings)
- Opus开发阶段审计.md (140+ findings, 18 P0 blockers)
- MiniMaxM3开发阶段审计.md (18 P0 blockers, focuses on executability)
- AirPlan/TODO.md (technical debt + 42 TODOs by phase)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

packages/runtime/src/storage/repositories/ToolRunRepository.ts

@@ -0,0 +1,179 @@
+/**
+ * ToolRunRepository - CRUD + list_by_task, list_by_origin_message for tool_runs table (§11)
+ *
+ * Implements Repository<ToolRunRecord, ToolRunInsert, ToolRunUpdate> per contracts §6.
+ *
+ * @module packages/runtime/src/storage/repositories/ToolRunRepository
+ */
+
+import type {
+  Repository,
+  TransactionHandle,
+  SessionID,
+  TaskID,
+  AgentID,
+  ToolRunID,
+  MessageID,
+  ISOTimeString,
+} from '@aircoding/contracts'
+
+import { DatabaseHandle } from '../MigrationRunner.js'
+
+// =============================================================================
+// Types - per db-schema §11
+// =============================================================================
+
+export type ToolRunStatus = 'running' | 'ok' | 'error' | 'cancelled'
+
+export interface ToolRunRecord {
+  id: ToolRunID
+  session_id: SessionID
+  task_id?: TaskID
+  agent_id?: AgentID
+  origin_message_id?: MessageID
+  tool_name: string
+  status: ToolRunStatus
+  input_json: string
+  output_json?: string
+  error_json?: string
+  started_at: ISOTimeString
+  completed_at?: ISOTimeString
+  duration_ms?: number
+  artifacts_json?: string
+  evidence_refs_json?: string
+  metadata_json?: string
+}
+
+export type ToolRunInsert = Omit<ToolRunRecord, 'id' | 'status'> & {
+  id?: ToolRunID
+}
+
+export type ToolRunUpdate = Partial<Omit<ToolRunRecord, 'id' | 'session_id' | 'tool_name' | 'started_at' | 'status'>>
+
+// =============================================================================
+// ToolRunRepository
+// =============================================================================
+
+export class ToolRunRepository implements Repository<ToolRunRecord, ToolRunInsert, ToolRunUpdate> {
+  private db: DatabaseHandle
+
+  constructor(db: DatabaseHandle) {
+    this.db = db
+  }
+
+  /**
+   * Get a tool run by ID.
+   */
+  async get(id: ToolRunID, _tx?: TransactionHandle): Promise<ToolRunRecord | undefined> {
+    const stmt = this.db.prepare('SELECT * FROM tool_runs WHERE id = ?')
+    const row = stmt.get(id) as ToolRunRecord | undefined
+    return row
+  }
+
+  /**
+   * Insert a new tool run. Status is set by EventStore projection (INV-1).
+   */
+  async insert(record: ToolRunInsert, _tx?: TransactionHandle): Promise<void> {
+    // Status is set by EventStore.project(), not by caller
+    const status: ToolRunStatus = 'running'
+
+    const stmt = this.db.prepare(`
+      INSERT INTO tool_runs (
+        id, session_id, task_id, agent_id, origin_message_id,
+        tool_name, status,
+        input_json, output_json, error_json,
+        started_at, completed_at, duration_ms,
+        artifacts_json, evidence_refs_json, metadata_json
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `)
+
+    stmt.run(
+      record.id,
+      record.session_id,
+      record.task_id ?? null,
+      record.agent_id ?? null,
+      record.origin_message_id ?? null,
+      record.tool_name,
+      status,
+      record.input_json,
+      record.output_json ?? null,
+      record.error_json ?? null,
+      record.started_at,
+      record.completed_at ?? null,
+      record.duration_ms ?? null,
+      record.artifacts_json ?? null,
+      record.evidence_refs_json ?? null,
+      record.metadata_json ?? null,
+    )
+  }
+
+  /**
+   * Update an existing tool run. Status changes only via EventStore projection (INV-1).
+   */
+  async update(id: ToolRunID, patch: ToolRunUpdate, _tx?: TransactionHandle): Promise<void> {
+    const fields: string[] = []
+    const values: unknown[] = []
+
+    // NOTE: status is NOT updatable here - only EventStore.project() writes status columns
+    if (patch.output_json !== undefined) {
+      fields.push('output_json = ?')
+      values.push(patch.output_json)
+    }
+    if (patch.error_json !== undefined) {
+      fields.push('error_json = ?')
+      values.push(patch.error_json)
+    }
+    if (patch.completed_at !== undefined) {
+      fields.push('completed_at = ?')
+      values.push(patch.completed_at)
+    }
+    if (patch.duration_ms !== undefined) {
+      fields.push('duration_ms = ?')
+      values.push(patch.duration_ms)
+    }
+    if (patch.artifacts_json !== undefined) {
+      fields.push('artifacts_json = ?')
+      values.push(patch.artifacts_json)
+    }
+    if (patch.evidence_refs_json !== undefined) {
+      fields.push('evidence_refs_json = ?')
+      values.push(patch.evidence_refs_json)
+    }
+    if (patch.metadata_json !== undefined) {
+      fields.push('metadata_json = ?')
+      values.push(patch.metadata_json)
+    }
+
+    if (fields.length === 0) {
+      return // Nothing to update
+    }
+
+    values.push(id)
+    const stmt = this.db.prepare(`UPDATE tool_runs SET ${fields.join(', ')} WHERE id = ?`)
+    stmt.run(...values)
+  }
+
+  // =============================================================================
+  // Extra methods
+  // =============================================================================
+
+  /**
+   * List tool runs for a specific task.
+   */
+  async list_by_task(task_id: TaskID): Promise<ToolRunRecord[]> {
+    const stmt = this.db.prepare(
+      'SELECT * FROM tool_runs WHERE task_id = ? ORDER BY started_at DESC',
+    )
+    return stmt.all(task_id) as ToolRunRecord[]
+  }
+
+  /**
+   * List tool runs for a specific origin message.
+   */
+  async list_by_origin_message(message_id: MessageID): Promise<ToolRunRecord[]> {
+    const stmt = this.db.prepare(
+      'SELECT * FROM tool_runs WHERE origin_message_id = ? ORDER BY started_at ASC',
+    )
+    return stmt.all(message_id) as ToolRunRecord[]
+  }
+}