fix(P0): close 15 blockers + add 26 regression tests; fix wiring schema regression

Phase A (security red lines) — CLOSED:
- B8: 3x command injection fixed (execFileSync + args array in CMake/CppBuilder/Cppcheck)
- B6: ToolRegistry permission bypass fixed (real task_scope/profile passed)
- B7: ACTION_BRANCHES this-binding crash fixed (instance method)
- B17: DeveloperLogEncryptor hardcoded 'dev-key' removed (throws if no key)
- B22: CommandRiskAnalyzer 'in' operator bug fixed (includes)
- B1: EventStore.project() transaction handle now passed to all repos
- B2: workspace projection illegal enum fixed (active/merged)
- B4: route_prefix separator unified to '/'
- B5: TaskAttempt column mapping fixed

Other blockers fixed:
- B3: project-level DB schema aligned to db-schema §20 (.air/local, learned_memories)
- B9: cpp.* tools registered through PermissionEngine path
- B11: Scheduler BLOCKED/CANCELLED states added
- B18: CapabilityTrustLevel 5-level enum aligned
- B19: PermissionEngine block/refuse/announce_then_run + grant_scope
- B20: Worker exit code 4 = parent_cancelled
- B24: project_id now randomUUID

Regression fix (introduced by B3 schema refactor):
- wiring.ts capture_debug_record/promote_memory_entry realigned to
  refactored DebugRecord/MemoryEntry interfaces (was compile-level decoupling)

Tests: 128 regression/unit tests pass (22 regression + 3 unit + 3 e2e suites)

Still open (tracked for next round): B10 (INV-2 outbox emit), B12 (Scheduler
event projection), B13 (MainAgent LLM classify), B14 (IPC envelope fields),
B15 (TUI OpenTUI), B16 (api_key strict), B21 (CLI init INV-3), B23 (e2e real),
B25 (MVP tools), B26 (ContextAssembler L6-L9)

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

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

@@ -64,8 +64,8 @@ export class ToolRunRepository implements Repository<ToolRunRecord, ToolRunInser
   /**
    * 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 = ?')
+  async get(id: ToolRunID, tx?: TransactionHandle): Promise<ToolRunRecord | undefined> {
+    const stmt = (tx?.db ?? this.db).prepare('SELECT * FROM tool_runs WHERE id = ?')
     const row = stmt.get(id) as ToolRunRecord | undefined
     return row
   }
@@ -73,11 +73,11 @@ export class ToolRunRepository implements Repository<ToolRunRecord, ToolRunInser
   /**
    * Insert a new tool run. Status is set by EventStore projection (INV-1).
    */
-  async insert(record: ToolRunInsert, _tx?: TransactionHandle): Promise<void> {
+  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(`
+    const stmt = (tx?.db ?? this.db).prepare(`
       INSERT INTO tool_runs (
         id, session_id, task_id, agent_id, origin_message_id,
         tool_name, status,
@@ -110,7 +110,7 @@ export class ToolRunRepository implements Repository<ToolRunRecord, ToolRunInser
   /**
    * Update an existing tool run. Status changes only via EventStore projection (INV-1).
    */
-  async update(id: ToolRunID, patch: ToolRunUpdate, _tx?: TransactionHandle): Promise<void> {
+  async update(id: ToolRunID, patch: ToolRunUpdate, tx?: TransactionHandle): Promise<void> {
     const fields: string[] = []
     const values: unknown[] = []
 
@@ -149,7 +149,7 @@ export class ToolRunRepository implements Repository<ToolRunRecord, ToolRunInser
     }
 
     values.push(id)
-    const stmt = this.db.prepare(`UPDATE tool_runs SET ${fields.join(', ')} WHERE id = ?`)
+    const stmt = (tx?.db ?? this.db).prepare(`UPDATE tool_runs SET ${fields.join(', ')} WHERE id = ?`)
     stmt.run(...values)
   }