trim: remove dead code and move large spec docs to attic

- Remove unused exports: renderProgress, formatTripleBoundaryCounterexample, clearCapturedRoutes
- Remove dead BUILTIN_PLUGIN_CONTRACTS constant (auto-registration removed earlier)
- Fix app-loader error messages to mention multiple export patterns
- Move to attic: protocol-extensions-spec, OUTBOUND_CONTRACT_MOCKING_SPEC, PLUGIN_CONTRACTS_SPEC, fastify-structure
- Build: clean | Tests: 849 pass, 0 fail

README.md

@@ -124,7 +124,7 @@ See [docs/llm-safe-adoption.md](docs/llm-safe-adoption.md) for templates and CI
 - [Qualify Mode](docs/qualify.md) — Scenarios, stateful testing, chaos
 - [Performance](docs/performance.md) — Repeatable benchmarks and CPU profiling
 - [LLM-Safe Adoption](docs/llm-safe-adoption.md) — Scaffolds and CI guards
-- [Protocol Extensions](docs/protocol-extensions-spec.md) — JWT, X.509, SPIFFE, WIMSE
+- [Protocol Extensions](docs/attic/protocol-extensions-spec.md) — JWT, X.509, SPIFFE, WIMSE
 
 ## License
 

SKILL.md

@@ -407,7 +407,7 @@ Then execute APOPHIS from the project test harness or CLI as appropriate. For mo
 1. `README.md` for canonical usage.
 2. `docs/getting-started.md` for quick setup.
 3. `docs/cli.md` and command docs for CLI flags and machine output.
-4. `docs/protocol-extensions-spec.md` for protocol-specific direction.
+4. `docs/attic/protocol-extensions-spec.md` for protocol-specific direction.
 
 ## Final Check
 

docs/auth-patterns.md

@@ -135,7 +135,7 @@ fastify.get('/wimse/wit', {
 })
 ```
 
-See `docs/protocol-extensions-spec.md` for full JWT extension configuration.
+See `docs/attic/protocol-extensions-spec.md` for full JWT extension configuration.
 
 ---
 

src/cli/commands/doctor/checks/routes.ts

@@ -116,8 +116,8 @@ export async function checkRouteDiscovery(options: RouteCheckOptions): Promise<R
         name: 'route-discovery',
         status: 'fail',
         message: `App file ${appFile} does not export a valid object.`,
-        detail: 'Ensure the app file exports a Fastify instance as default.',
+        detail: 'Ensure the app file exports a Fastify instance or a factory function.',
-        remediation: 'Export your Fastify instance as default: export default app;',
+        remediation: 'Export your Fastify instance: export default app; or export const createApp = () => app; or module.exports = app;',
         mode: 'all',
       };
     }

src/cli/commands/qualify/index.ts

@@ -642,7 +642,7 @@ export async function qualifyCommand(
       }
       return {
         exitCode: USAGE_ERROR,
-        message: 'No Fastify app found. Ensure app.js exports a Fastify instance.',
+        message: 'No Fastify app found. Ensure app.js exports a Fastify instance or a factory function.\n\nSupported patterns:\n  export default app\n  export const createApp = () => app\n  module.exports = app',
       }
     }
 

src/cli/commands/verify/index.ts

@@ -468,7 +468,7 @@ export async function verifyCommand(
       const errorMessage = err instanceof Error ? err.message : String(err)
       return {
         exitCode: USAGE_ERROR,
-        message: `No Fastify app found. Ensure app.js exports a Fastify instance.\n\nError: ${errorMessage}\n\nNext:\n  Run \`apophis init\` to scaffold a working app.js and config.`,
+        message: `No Fastify app found. Ensure app.js exports a Fastify instance or a factory function.\n\nSupported patterns:\n  export default app\n  export const createApp = () => app\n  module.exports = app\n\nError: ${errorMessage}\n\nNext:\n  Run \`apophis init\` to scaffold a working app.js and config.`,
       }
     }
 

src/cli/renderers/human.ts

@@ -183,29 +183,6 @@ function generateNextSteps(failure: FailureRecord): string {
 // Progress and summary rendering
 // ---------------------------------------------------------------------------
 
-/**
- * Render progress for a running command.
- * Safe for CI (no spinners, just text updates).
- */
-export function renderProgress(
-  current: number,
-  total: number,
-  label: string,
-  ctx: OutputContext,
-): string {
-  const c = getColorizer(ctx);
-  const pct = total > 0 ? Math.round((current / total) * 100) : 0;
-
-  if (ctx.isCI || !ctx.isTTY) {
-    // CI mode: simple text, no spinner
-    return `${label} [${current}/${total}] ${pct}%`;
-  }
-
-  // TTY mode: with color
-  const bar = renderProgressBar(current, total, 20, ctx);
-  return `${c.dim(label)} ${bar} ${c.bold(`${pct}%`)}`;
-}
-
 /**
  * Render a simple ASCII progress bar.
  */

src/domain/discovery.ts

@@ -87,9 +87,3 @@ export const discoverRoutes = (instance: { routes?: Array<{ method: string; url:
   // Fastify 5 fallback: routes registered before plugin
   return discoverRoutesFallback(instance)
 }
-/**
- * Clear captured routes for an instance (useful for testing).
- */
-export const clearCapturedRoutes = (instance: object): void => {
-  capturedRoutes.delete(instance)
-}

src/domain/plugin-contracts.ts

@@ -143,46 +143,6 @@ export class PluginContractRegistry {
   }
 }
 // ============================================================================
-// Built-in Plugin Contracts
-// ============================================================================
-export const BUILTIN_PLUGIN_CONTRACTS: Record<string, PluginContractSpec> = {
-  '@fastify/auth': {
-    appliesTo: '**',
-    hooks: {
-      onRequest: {
-        requires: ['request_headers(this).authorization != null'],
-      },
-    },
-  },
-  '@fastify/compress': {
-    appliesTo: '**',
-    hooks: {
-      onSend: {
-        ensures: ['response_headers(this).content-encoding != null'],
-      },
-    },
-  },
-  '@fastify/cors': {
-    appliesTo: '**',
-    hooks: {
-      onRequest: {
-        ensures: ['response_headers(this).access-control-allow-origin != null'],
-      },
-    },
-  },
-  '@fastify/rate-limit': {
-    appliesTo: '**',
-    hooks: {
-      onRequest: {
-        ensures: [
-          'response_headers(this).x-ratelimit-limit != null',
-          'response_headers(this).x-ratelimit-remaining != null',
-        ],
-      },
-    },
-  },
-}
-// ============================================================================
 // Factory
 // ============================================================================
 export function createPluginContractRegistry(): PluginContractRegistry {

src/domain/triple-boundary-testing.ts

@@ -360,47 +360,3 @@ export function applyChaosToAllResponses(
     )
   })
 }
-// ============================================================================
-// Formatting
-// ============================================================================
-export function formatTripleBoundaryCounterexample(result: TripleBoundaryResult): string {
-  const lines: string[] = []
-  lines.push('Triple-boundary counterexample:')
-  lines.push('')
-  lines.push(`Route: ${result.command.route.method} ${result.command.route.path}`)
-  lines.push('')
-  lines.push('Request:')
-  lines.push(JSON.stringify(result.command.request, null, 2))
-  lines.push('')
-  if (result.command.dependencyResponses.length > 0) {
-    lines.push('Dependency responses:')
-    for (const dep of result.command.dependencyResponses) {
-      lines.push(`  ${dep.contractName}: ${dep.statusCode}`)
-      lines.push(`    ${JSON.stringify(dep.body)}`)
-    }
-    lines.push('')
-  }
-  if (result.command.chaosEvents.length > 0) {
-    lines.push('Chaos events:')
-    for (const chaos of result.command.chaosEvents) {
-      if (chaos.type === 'none') continue
-      lines.push(`  ${chaos.type}`)
-      if (chaos.contractName) lines.push(`    Target: ${chaos.contractName}`)
-      if (chaos.delayMs) lines.push(`    Delay: ${chaos.delayMs}ms`)
-      if (chaos.statusCode) lines.push(`    Status: ${chaos.statusCode}`)
-      if (chaos.corruptionStrategy) lines.push(`    Corruption: ${chaos.corruptionStrategy}`)
-      if (chaos.corruptionField) lines.push(`    Field: ${chaos.corruptionField}`)
-    }
-    lines.push('')
-  }
-  if (result.failureBoundary) {
-    lines.push(`Failure boundary: ${result.failureBoundary}`)
-  }
-  if (result.failureDescription) {
-    lines.push(`Description: ${result.failureDescription}`)
-  }
-  if (result.error) {
-    lines.push(`Error: ${result.error}`)
-  }
-  return lines.join('\n')
-}