fix: address code-level issues from subworker audit

- Remove unused generationProfile parameter from verify runner
- Integrate PluginContractRegistry into petit-runner and stateful-runner
- Add deterministic hashStringToSeed to doctor (replaces Math.random())
- Create and pass CleanupManager in stateful-handler
- Remove unconditional auto-registration of built-in plugin contracts
  (they were too aggressive; users can register via opts.pluginContracts)
- Build: clean | Tests: 849 pass, 0 fail

src/plugin/index.ts

@@ -13,7 +13,7 @@ import { registerValidationHooks, storeRouteContract } from '../infrastructure/h
 import { extractContract } from '../domain/contract.js'
 import { createExtensionRegistry } from '../extension/registry.js'
 import type { ApophisExtension } from '../extension/types.js'
-import { createPluginContractRegistry, BUILTIN_PLUGIN_CONTRACTS } from '../domain/plugin-contracts.js'
+import { createPluginContractRegistry } from '../domain/plugin-contracts.js'
 import type { PluginContractRegistry } from '../domain/plugin-contracts.js'
 import { OutboundContractRegistry } from '../domain/outbound-contracts.js'
 import { createOutboundMockRuntime, type OutboundMockRuntime } from '../infrastructure/outbound-mock-runtime.js'
@@ -75,10 +75,6 @@ export const apophisPlugin = async (fastify: FastifyInstance, opts: ApophisOptio
   // Initialize scope registry with explicit config or empty
   const scope = new ScopeRegistry(opts.scopes ?? {})
   const cleanupManager = new CleanupManager(fastify, scope, opts.cleanup ?? false)
-  // Register built-in plugin contracts
-  for (const [name, spec] of Object.entries(BUILTIN_PLUGIN_CONTRACTS)) {
-    pluginContractRegistry.register(name, spec)
-  }
   // Register user-provided plugin contracts
   if (opts.pluginContracts) {
     for (const [name, spec] of Object.entries(opts.pluginContracts)) {