fix: tsc 0 errors + depcruise 0 violations + all GA blockers closed

Changes (37 files, +1159/-587):
- tsconfig: moduleResolution bundler + paths alias for bun:sqlite
- bun-sqlite.ts: type shim replacing stale declare module .d.ts
- All 7 tool files: ToolDefinition alignment (version, output_schema,
  ToolPermissionSpec read_paths/write_paths, ToolCall.call_id)
- 2 adapters: ProviderAdapter implements + ProviderCapabilityMatrix shape
  (provider_kind, enabled, quality_tier, cost_tier, conversion)
- PathClassifier: 9 categories aligned (credential_store, project_air_*)
- CommandRiskAnalyzer: remove unused imports
- Recovery: Database field + scanOrphanReferences FK-off 8 invariants
- Scheduler: rebuild_from_db from session DB tasks
- ProjectionStore: 20+ event types, subscribe, rebuild from repos
- MigrationRunner: constructor accepts optional db_path
- e2e.ts: replaced hardcoded ✅ with 14 real test/check gates
- wiring.ts: eventIngestor.ingest (durable path, INV-2)
- init.ts: ToolRegistry+PermissionEngine path (INV-3)
- TUI: local ProjectionClient (INV-4)
- MainAgent: classify_via_llm with real ProviderManager invocation
- WorkerMessage: kind/session_id/agent_id/correlation_id (contracts §10)
- WorkerProcess exit code 4 = parent_cancelled

Validation gates:
- tsc --noEmit: 0 errors
- depcruise: 0 violations (28 modules)
- tests: 169/169 pass

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

packages/runtime/src/tools/shell/index.ts

@@ -12,8 +12,10 @@ import type { ToolDefinition, ToolCall, ToolResultEnvelope, ISOTimeString } from
 
 export const shell_run: ToolDefinition = {
   name: 'shell.run',
-  category: 'execute',
+  category: 'shell',
   description: 'Run a shell command',
+  version: 1,
+  output_schema: { type: 'object', properties: {}, required: [] },
   input_schema: {
     type: 'object',
     properties: {
@@ -24,7 +26,7 @@ export const shell_run: ToolDefinition = {
     },
     required: ['command']
   },
-  permissions: { read: false, write: false, network: true },
+  permissions: { network: true },
   streaming: true
 }
 
@@ -43,11 +45,9 @@ export function createShellExecutor(project_root: string) {
 
       // Emit command.started event
       yield {
-        call_id: call.id,
-        tool_name: 'shell.run',
-        type: 'text',
-        content: { event: 'command.started', command, cwd },
-        metadata: { timestamp, streaming: true }
+        status: 'ok',
+        output: { event: 'command.started', command, cwd },
+        metadata: { timestamp, streaming: true, call_id: call.call_id, tool_name: 'shell.run' }
       }
 
       // Execute command
@@ -97,10 +97,8 @@ export function createShellExecutor(project_root: string) {
 
       // Emit command.completed event
       yield {
-        call_id: call.id,
-        tool_name: 'shell.run',
-        type: final_code === 0 ? 'text' : 'error',
-        content: {
+        status: final_code === 0 ? 'ok' : 'error',
+        output: {
           event: 'command.completed',
           exit_code: final_code,
           stdout: stdout.slice(-50000), // Last 50KB