fix: remove destructive migrate rewrite, add replay source attribution and warning drain

src/cli/commands/migrate/rewriters/route-rewriter.ts

@@ -2,7 +2,7 @@
  * Route rewriter for APOPHIS migrate command.
  *
  * Responsibilities:
- * - Rewrite route schema annotations (e.g., x-validate-runtime → runtime)
+ * - Rewrite route schema annotations
  * - Preserve schema structure and formatting
  * - Handle annotations in Fastify route definitions
  * - Detect ambiguous annotations and require manual choice
@@ -40,10 +40,12 @@ export interface AmbiguousRoutePattern {
 
 /**
  * Mapping of deprecated route schema annotations to their modern equivalents.
+ * x-validate-runtime is intentionally NOT here — it is the current, active annotation
+ * used by contract.ts and hook-validator.ts for per-route runtime validation opt-out.
+ * Rewriting it to 'runtime' would break it, since 'runtime' is a top-level plugin
+ * config option, not a valid route schema annotation.
  */
-export const LEGACY_ROUTE_ANNOTATIONS: Record<string, string> = {
-  'x-validate-runtime': 'runtime',
-};
+export const LEGACY_ROUTE_ANNOTATIONS: Record<string, string> = {};
 
 /**
  * Ambiguous route patterns that require manual choice.

src/cli/commands/replay/index.ts

@@ -73,33 +73,44 @@ function formatHumanOutput(result: ReplayResult, artifact: Artifact): string {
     w.includes('Artifact cwd no longer exists')
   )
 
+  function formatFailure(label: string, failure: FailureRecord | undefined): void {
+    if (!failure) return
+    lines.push(label)
+    lines.push(`  Route: ${failure.route}`)
+    if (failure.source && failure.source !== 'route') {
+      lines.push(`  Source: ${failure.source}`)
+    }
+    if (failure.contract) {
+      lines.push(`  Contract: ${failure.contract}`)
+    }
+    if (failure.expected) {
+      lines.push(`  Expected: ${failure.expected}`)
+    }
+    if (failure.observed) {
+      lines.push(`  Observed: ${failure.observed}`)
+    }
+  }
+
   if (result.reproduced) {
     lines.push('Replay reproduced the original failure.')
     lines.push('')
-    lines.push('Original failure')
-    lines.push(`  Route: ${result.originalFailure?.route}`)
-    lines.push(`  Contract: ${result.originalFailure?.contract}`)
-    lines.push(`  Expected: ${result.originalFailure?.expected}`)
-    lines.push(`  Observed: ${result.originalFailure?.observed}`)
+    formatFailure('Original failure', result.originalFailure)
     lines.push(`  Seed: ${artifact.seed}`)
   } else if (result.newFailure) {
     lines.push('Replay produced a different result.')
     lines.push('')
-    lines.push('Original failure')
-    lines.push(`  Route: ${result.originalFailure?.route}`)
-    lines.push(`  Contract: ${result.originalFailure?.contract}`)
+    formatFailure('Original failure', result.originalFailure)
     lines.push('')
-    lines.push('New result')
-    lines.push(`  Route: ${result.newFailure.route}`)
-    lines.push(`  Contract: ${result.newFailure.contract}`)
-    lines.push(`  Expected: ${result.newFailure.expected}`)
-    lines.push(`  Observed: ${result.newFailure.observed}`)
+    formatFailure('New result', result.newFailure)
     lines.push(`  Seed: ${artifact.seed}`)
   } else {
     lines.push('Replay passed — failure no longer reproduces.')
     lines.push('')
     lines.push('Original failure')
     lines.push(`  Route: ${result.originalFailure?.route}`)
+    if (result.originalFailure?.source && result.originalFailure.source !== 'route') {
+      lines.push(`  Source: ${result.originalFailure.source}`)
+    }
     lines.push(`  Contract: ${result.originalFailure?.contract}`)
     lines.push(`  Seed: ${artifact.seed}`)
   }
@@ -299,6 +310,14 @@ async function executeReplay(
     pluginContractRegistry,
   })
 
+  // Drain plugin contract registry warnings (missing extensions, etc.)
+  if (pluginContractRegistry?.drainWarnings) {
+    const pcrWarnings = pluginContractRegistry.drainWarnings()
+    if (pcrWarnings.length > 0) {
+      warnings.push(...pcrWarnings)
+    }
+  }
+
   // If no routes matched, or route found but no contracts (plugin not registered before routes),
   // try direct contract execution
   if (runResult.noRoutesMatched || runResult.noContractsFound) {
@@ -403,6 +422,7 @@ async function executeReplay(
           observed: newFailure.observed,
           seed: artifact.seed || 42,
           replayCommand: `apophis replay --artifact ${artifactPath}`,
+          source: newFailure.source,
         },
         warnings,
       }, artifact),
@@ -416,6 +436,7 @@ async function executeReplay(
         observed: newFailure.observed,
         seed: artifact.seed || 42,
         replayCommand: `apophis replay --artifact ${artifactPath}`,
+        source: newFailure.source,
       },
     }
   }

src/cli/commands/verify/index.ts

@@ -123,6 +123,7 @@ function buildArtifact(
       seed: options.seed,
       replayCommand: `apophis replay --artifact ${f.artifactPath || '<artifact-path-unavailable>'}`,
       category: f.category ?? (f.observed ? classifyError(f.observed) : ErrorTaxonomy.RUNTIME),
+      source: f.source,
     }
   })
 

src/cli/commands/verify/runner.ts

@@ -40,6 +40,8 @@ export interface VerifyFailure {
   artifactPath?: string
   formula?: string
   category?: string
+  /** Source of the contract: 'route' or 'plugin:name' */
+  source?: string
 }
 
 export interface VerifyRunResult {
@@ -649,6 +651,7 @@ export async function runVerify(deps: VerifyRunnerDeps): Promise<VerifyRunResult
                   observed: diagnostic.observed,
                   formula: diagnostic.formula,
                   category: diagnostic.category,
+                  source: route.formulaSources?.[formula],
                 })
               } else {
                 passedCount++
@@ -664,6 +667,7 @@ export async function runVerify(deps: VerifyRunnerDeps): Promise<VerifyRunResult
                 observed: diagnostic.observed,
                 formula: diagnostic.formula,
                 category: diagnostic.category,
+                source: route.formulaSources?.[formula],
               })
             }
           }

src/cli/core/types.ts

@@ -195,6 +195,8 @@ export interface FailureRecord {
   category?: string;
   diff?: string;
   actual?: string;
+  /** Source of the contract: 'route' or 'plugin:name' */
+  source?: string;
 }
 
 /**

src/test/cli/migrate-reliability.test.ts

@@ -469,9 +469,9 @@ test('config rewriter replaces legacy fields', () => {
   }
 });
 // ---------------------------------------------------------------------------
-// Test 12: Route rewriter detects x-validate-runtime annotation
+// Test 12: x-validate-runtime is NOT a legacy annotation (it is the current, active format)
 // ---------------------------------------------------------------------------
-test('route rewriter detects x-validate-runtime annotation', () => {
+test('x-validate-runtime is current annotation, not legacy', () => {
   const dir = createTempDir();
   try {
     const content = `export default {
@@ -481,18 +481,7 @@ test('route rewriter detects x-validate-runtime annotation', () => {
 };`;
     writeFileSync(resolve(dir, 'test.routes.js'), content);
     const items = detectLegacyRouteAnnotations(content, 'test.routes.js');
-    assert.strictEqual(items.length, 1, 'Should detect 1 legacy annotation');
-    const firstItem = items[0];
-    assert.ok(firstItem, 'Expected one migration item');
-    assert.strictEqual(firstItem.legacy, 'x-validate-runtime');
-    assert.strictEqual(firstItem.replacement, 'runtime');
-    const result = rewriteRouteAnnotations(
-      resolve(dir, 'test.routes.js'),
-      items,
-    );
-    assert.strictEqual(result.modified, true, 'Should modify content');
-    assert.ok(result.content.includes("'runtime'"), 'Should have runtime');
-    assert.ok(!result.content.includes('x-validate-runtime'), 'Should not have legacy annotation');
+    assert.strictEqual(items.length, 0, 'x-validate-runtime must not be detected as legacy — it is the current annotation');
   } finally {
     cleanup(dir);
   }