@codeyam/codeyam-cli 0.1.0-staging.483fdc2 → 0.1.0-staging.49751cb

package/analyzer-template/packages/analyze/src/lib/files/scenarios/mergeInDependentDataStructure.ts

@@ -4,6 +4,7 @@ import {
 } from '~codeyam/ai';
 import { cleanKnownObjectFunctionsFromMapping } from '~codeyam/ai';
 import { DataStructure, Entity, ReadonlyAnalysis } from '~codeyam/types';
+import { transformationTracer } from './TransformationTracer';
 
 export interface DataStructureInfo {
   signatureSchema: { [key: string]: string };
@@ -40,6 +41,36 @@ function getTypeParameter(functionName: string): string | null {
   return null;
 }
 
+/**
+ * Check if a schema path contains a Set/Map collection method call.
+ * Paths like `.has(articleId)`, `.delete(articleId)`, `.add(articleId)` represent
+ * membership checks on Sets/Maps, not meaningful data flow for schema generation.
+ * These create massive combinatorial explosions when every filter field (filterRatings,
+ * filterPublications, filterAuthors, etc.) × every method (has, delete, add) gets
+ * tracked as a separate equivalency.
+ */
+const COLLECTION_METHOD_PATTERN = /\.(?:has|delete|add|clear|get|set)\(/;
+function isCollectionMethodPath(path: string): boolean {
+  return COLLECTION_METHOD_PATTERN.test(path);
+}
+
+/**
+ * Check if a path contains an inline object literal inside a function call argument.
+ * e.g., setUndoEntry({ label: '...', undo: () => {} }) has '{' inside '(' ')'.
+ * These paths are call-site snapshots where the source code text was captured
+ * as the path. They don't represent schema structure and are very expensive to
+ * parse (avg 319 chars). They account for ~55% of equivalencies in complex entities.
+ */
+const INLINE_OBJECT_ARG_PATTERN = /\([^)]*\{[^}]*:/;
+function hasInlineObjectArg(path: string): boolean {
+  // Match function calls containing object literals with key-value pairs.
+  // Pattern: open paren, then { with a : inside before closing }.
+  // e.g., setUndoEntry({ label: '...' }) matches
+  // e.g., find(item) does NOT match
+  // e.g., fn({a:1, b:2}) matches
+  return INLINE_OBJECT_ARG_PATTERN.test(path);
+}
+
 // Primitive types that should not have child paths
 const PRIMITIVE_TYPES = new Set([
   'number',
@@ -51,6 +82,7 @@ const PRIMITIVE_TYPES = new Set([
 
 // Check if a type string represents a primitive type
 // Handles union types like "string | undefined" or "number | null"
+// Also handles string literal unions like "'suggestion' | 'warning' | 'tip'"
 function isPrimitiveType(typeStr: string): boolean {
   if (PRIMITIVE_TYPES.has(typeStr)) {
     return true;
@@ -58,13 +90,26 @@ function isPrimitiveType(typeStr: string): boolean {
   // Check union types - if ALL parts of the union are primitives, it's primitive
   // e.g., "string | undefined" -> ["string", "undefined"] -> both are primitive -> true
   // e.g., "object | null" -> ["object", "null"] -> object is not primitive -> false
+  // e.g., "'suggestion' | 'warning'" -> string literal union -> true
   if (typeStr.includes('|')) {
     const parts = typeStr.split('|').map((p) => p.trim());
-    return parts.every((part) => PRIMITIVE_TYPES.has(part));
+    return parts.every(
+      (part) =>
+        PRIMITIVE_TYPES.has(part) ||
+        // String literal values like 'suggestion', 'warning' are primitives
+        (part.startsWith("'") && part.endsWith("'")),
+    );
   }
   return false;
 }
 
+// Extract signature index from a path like "signature[0]" or "signature[0].foo"
+// Returns the index number or undefined if not a signature path
+function extractSignatureIndex(path: string): number | undefined {
+  const match = path.match(/^signature\[(\d+)\]/);
+  return match ? parseInt(match[1], 10) : undefined;
+}
+
 // Check if a new schema path would go through a primitive type
 // e.g., if schema has 'entities[].scenarioCount': 'number', then
 // 'entities[].scenarioCount.sha' would go through a primitive and should be rejected
@@ -102,9 +147,21 @@ function pathPartMatches(pathPart: string, schemaPathPart: string): boolean {
 function bestValueFromOptions(options: Array<string | undefined>) {
   options = options.filter(Boolean) as string[];
 
-  const known = options.find((o) => !o.includes('unknown'));
-  if (known) {
-    return known;
+  const known = options.filter((o) => !o.includes('unknown'));
+  if (known.length > 0) {
+    // Among known values, prefer string literal unions over bare primitives.
+    // e.g., "'draft' | 'inProgress' | 'paused' | 'completed'" is more specific than "string".
+    // This handles cases where a dependency schema has a bare type like "string" but the
+    // child entity's analysis has the actual literal union from TypeScript type resolution.
+    if (known.length > 1 && known.some((o) => PRIMITIVE_TYPES.has(o))) {
+      const literalUnion = known.find(
+        (o) => !PRIMITIVE_TYPES.has(o) && o.includes("'"),
+      );
+      if (literalUnion) {
+        return literalUnion;
+      }
+    }
+    return known[0];
   }
 
   const notUnknown = options.find((o) => o !== 'unknown');
@@ -115,12 +172,31 @@ function bestValueFromOptions(options: Array<string | undefined>) {
   return options[0] ?? 'unknown';
 }
 
+/** Timeout (ms) for the merge operation. Throws DataStructureTimeoutError if exceeded.
+ *  All successful merges complete in <300ms. Anything exceeding 2s is pathological. */
+const MERGE_TIMEOUT_MS = 2_000;
+
+/** Cap for schema size during postfix application and dep copy.
+ *  Successful merges produce <3K ret keys. Beyond 5K, further entries
+ *  are cross-products of unrelated equivalencies — noise, not signal. */
+const SCHEMA_KEY_CAP = 5_000;
+
+export class DataStructureTimeoutError extends Error {
+  constructor(entityName: string, elapsedMs: number) {
+    super(
+      `Data structure merge timed out for ${entityName} after ${Math.round(elapsedMs / 1000)}s (limit: ${MERGE_TIMEOUT_MS / 1000}s)`,
+    );
+    this.name = 'DataStructureTimeoutError';
+  }
+}
+
 export default function mergeInDependentDataStructure({
   importedExports,
   dependentAnalyses,
   rootScopeName,
   dataStructure,
   dependencySchemas,
+  timeoutMs = MERGE_TIMEOUT_MS,
 }: {
   importedExports: Pick<
     Entity['metadata']['importedExports'][0],
@@ -142,7 +218,23 @@ export default function mergeInDependentDataStructure({
       [name: string]: DataStructureInfo;
     };
   };
+  /** Override the default timeout (ms). Set to 0 to disable. */
+  timeoutMs?: number;
 }) {
+  const mergeStartTime = Date.now();
+  const mergeDeadline = timeoutMs > 0 ? mergeStartTime + timeoutMs : 0;
+
+  /** Call in hot loops. Throws DataStructureTimeoutError if deadline exceeded.
+   *  Date.now() is ~20ns — negligible vs the ms-scale string ops in each iteration. */
+  const checkDeadline = () => {
+    if (!mergeDeadline) return;
+    if (Date.now() > mergeDeadline) {
+      throw new DataStructureTimeoutError(
+        rootScopeName,
+        Date.now() - mergeStartTime,
+      );
+    }
+  };
   const mergedDataStructure: Omit<
     DataStructure,
     'equivalentSignatureVariables'
@@ -155,1401 +247,1865 @@ export default function mergeInDependentDataStructure({
     environmentVariables: [...(dataStructure.environmentVariables || [])],
   };
 
-  // Build a set of functions that have multiple DIFFERENT type parameters.
-  // For these functions, we must NOT normalize paths to avoid merging different schemas.
-  // e.g., if we have both useFetcher<{ data: UserData }>() and useFetcher<{ data: ConfigData }>(),
-  // they must stay separate and not both become 'returnValue'.
-  const functionsWithMultipleTypeParams = new Set<string>();
-  const typeParamsByFunction: Record<string, Set<string>> = {};
-
-  // Helper to scan a schema for type parameters
-  const scanSchemaForTypeParams = (schema: { [key: string]: string }) => {
-    for (const schemaPath of Object.keys(schema ?? {})) {
-      const parts = splitOutsideParenthesesAndArrays(schemaPath);
-      if (parts.length > 0) {
-        const firstPart = parts[0];
-        const typeParam = getTypeParameter(firstPart);
-        if (typeParam) {
-          const baseName = cleanFunctionName(firstPart);
-          typeParamsByFunction[baseName] ||= new Set();
-          typeParamsByFunction[baseName].add(typeParam);
-          if (typeParamsByFunction[baseName].size > 1) {
-            functionsWithMultipleTypeParams.add(baseName);
+  try {
+    // Build a set of functions that have multiple DIFFERENT type parameters.
+    // For these functions, we must NOT normalize paths to avoid merging different schemas.
+    // e.g., if we have both useFetcher<{ data: UserData }>() and useFetcher<{ data: ConfigData }>(),
+    // they must stay separate and not both become 'returnValue'.
+    const functionsWithMultipleTypeParams = new Set<string>();
+    const typeParamsByFunction: Record<string, Set<string>> = {};
+
+    // Helper to scan a schema for type parameters
+    const scanSchemaForTypeParams = (schema: { [key: string]: string }) => {
+      for (const schemaPath of Object.keys(schema ?? {})) {
+        const parts = splitOutsideParenthesesAndArrays(schemaPath);
+        if (parts.length > 0) {
+          const firstPart = parts[0];
+          const typeParam = getTypeParameter(firstPart);
+          if (typeParam) {
+            const baseName = cleanFunctionName(firstPart);
+            typeParamsByFunction[baseName] ||= new Set();
+            typeParamsByFunction[baseName].add(typeParam);
+            if (typeParamsByFunction[baseName].size > 1) {
+              functionsWithMultipleTypeParams.add(baseName);
+            }
           }
         }
       }
-    }
-  };
+    };
 
-  // Scan the root entity's schema
-  scanSchemaForTypeParams(dataStructure.returnValueSchema);
+    // Scan the root entity's schema
+    scanSchemaForTypeParams(dataStructure.returnValueSchema);
 
-  // Also scan all dependency schemas for type parameters
-  for (const filePath of Object.keys(dependencySchemas ?? {})) {
-    for (const name of Object.keys(dependencySchemas[filePath] ?? {})) {
-      scanSchemaForTypeParams(
-        dependencySchemas[filePath][name]?.returnValueSchema,
-      );
+    // Also scan all dependency schemas for type parameters
+    for (const filePath of Object.keys(dependencySchemas ?? {})) {
+      for (const name of Object.keys(dependencySchemas[filePath] ?? {})) {
+        scanSchemaForTypeParams(
+          dependencySchemas[filePath][name]?.returnValueSchema,
+        );
+      }
     }
-  }
 
-  let equivalentSchemaPaths: {
-    equivalentRoots: {
-      schemaRootPath: string;
-      function?: { filePath?: string; name: string };
-      postfix?: string;
-    }[];
-    equivalentPostfixes: Record<string, string>;
-  }[] = [];
-
-  // Pre-build a lookup map from cleaned function name to dependency for O(1) lookups.
-  // This avoids O(n) linear search in findRelevantDependency which was causing O(n²) performance.
-  const dependencyByCleanedName = new Map<
-    string,
-    (typeof importedExports)[0]
-  >();
-  for (const dep of importedExports) {
-    const cleanedName = cleanFunctionName(dep.name);
-    if (!dependencyByCleanedName.has(cleanedName)) {
-      dependencyByCleanedName.set(cleanedName, dep);
-    }
-  }
+    let equivalentSchemaPaths: {
+      equivalentRoots: {
+        schemaRootPath: string;
+        function?: { filePath?: string; name: string };
+        postfix?: string;
+      }[];
+      equivalentPostfixes: Record<string, string>;
+    }[] = [];
+
+    // O(1) index for findOrCreateEquivalentSchemaPathsEntry.
+    // Maps "(rootPath)::(normalizedFuncName)" → the entry containing that root.
+    // This replaces the O(E) linear search that was causing O(E²) gather performance.
+    const espIndex = new Map<string, (typeof equivalentSchemaPaths)[0]>();
+    const espIndexKey = (path: string, functionName: string | undefined) => {
+      const normalized = cleanFunctionName(functionName);
+      const funcKey =
+        normalized === rootScopeName ? '__self__' : normalized || '__self__';
+      return `${path}::${funcKey}`;
+    };
+    const updateEspIndex = (entry: (typeof equivalentSchemaPaths)[0]) => {
+      for (const root of entry.equivalentRoots) {
+        const funcName = root.function?.name ?? rootScopeName;
+        espIndex.set(espIndexKey(root.schemaRootPath, funcName), entry);
+      }
+    };
 
-  const findRelevantDependency = (functionName: any) => {
-    return dependencyByCleanedName.get(cleanFunctionName(functionName));
-  };
+    // Pre-build a lookup map from cleaned function name to dependency for O(1) lookups.
+    // This avoids O(n) linear search in findRelevantDependency which was causing O(n²) performance.
+    const dependencyByCleanedName = new Map<
+      string,
+      (typeof importedExports)[0]
+    >();
+    for (const dep of importedExports) {
+      const cleanedName = cleanFunctionName(dep.name);
+      if (!dependencyByCleanedName.has(cleanedName)) {
+        dependencyByCleanedName.set(cleanedName, dep);
+      }
+    }
 
-  const findRelevantDependentDataStructure = (functionName: any) => {
-    const dependency = findRelevantDependency(functionName);
-    if (!dependency) return;
+    const findRelevantDependency = (functionName: any) => {
+      return dependencyByCleanedName.get(cleanFunctionName(functionName));
+    };
 
-    return dependencySchemas?.[dependency.filePath]?.[dependency.name];
-  };
+    const findRelevantDependentDataStructure = (functionName: any) => {
+      const dependency = findRelevantDependency(functionName);
+      if (!dependency) return;
 
-  const findRelevantDependentAnalysisDataStructure = (functionName: any) => {
-    const dependency = findRelevantDependency(functionName);
-    if (!dependency) return;
+      return dependencySchemas?.[dependency.filePath]?.[dependency.name];
+    };
 
-    const dependentAnalysis =
-      dependentAnalyses[dependency.filePath]?.[dependency.name];
-    if (!dependentAnalysis?.metadata?.mergedDataStructure) {
-      return;
-    }
+    const findRelevantDependentAnalysisDataStructure = (functionName: any) => {
+      const dependency = findRelevantDependency(functionName);
+      if (!dependency) return;
 
-    return dependentAnalysis.metadata.mergedDataStructure;
-  };
+      const dependentAnalysis =
+        dependentAnalyses[dependency.filePath]?.[dependency.name];
+      if (!dependentAnalysis?.metadata?.mergedDataStructure) {
+        return;
+      }
 
-  const findOrCreateDependentSchemas = (dependency: {
-    filePath?: string;
-    name: string;
-  }) => {
-    const { filePath, name } = dependency;
-    mergedDataStructure.dependencySchemas[filePath] ||= {};
-    mergedDataStructure.dependencySchemas[filePath][name] ||= {
-      signatureSchema: {},
-      returnValueSchema: {},
+      return dependentAnalysis.metadata.mergedDataStructure;
     };
 
-    return mergedDataStructure.dependencySchemas[filePath][name];
-  };
+    const findOrCreateDependentSchemas = (dependency: {
+      filePath?: string;
+      name: string;
+    }) => {
+      const { filePath, name } = dependency;
+      mergedDataStructure.dependencySchemas[filePath] ||= {};
+      mergedDataStructure.dependencySchemas[filePath][name] ||= {
+        signatureSchema: {},
+        returnValueSchema: {},
+      };
 
-  const cleanSchema = (schema: { [key: string]: string }) => {
-    cleanKnownObjectFunctionsFromMapping(schema);
-  };
+      return mergedDataStructure.dependencySchemas[filePath][name];
+    };
+
+    const cleanSchema = (
+      schema: { [key: string]: string },
+      context?: Record<string, any>,
+    ) => {
+      transformationTracer.traceSchemaTransform(
+        rootScopeName,
+        'cleanKnownObjectFunctionsFromMapping',
+        schema,
+        cleanKnownObjectFunctionsFromMapping,
+        context,
+      );
+    };
 
-  const translatePath = (path: string, dependencyName: string) => {
-    if (path.startsWith(dependencyName)) {
-      const pathParts = splitOutsideParenthesesAndArrays(path);
-      if (pathParts.length > 1) {
-        if (pathParts[1].startsWith('functionCallReturnValue')) {
-          // Check if this function has multiple DIFFERENT type parameters.
-          // If so, DON'T normalize to returnValue - keep the full path to avoid
-          // merging different type-parameterized variants together.
-          // e.g., useFetcher<{ data: UserData }>().functionCallReturnValue.data
-          // should NOT be merged with useFetcher<{ data: ConfigData }>().functionCallReturnValue.data
-          const baseName = cleanFunctionName(pathParts[0]);
-          if (functionsWithMultipleTypeParams.has(baseName)) {
-            return path; // Keep the original path with type parameters
+    // Cache translatePath results — the same path is often translated multiple times
+    // (once per equivalency entry that references it). Avoids redundant
+    // splitOutsideParenthesesAndArrays calls on long paths.
+    const translatePathCache = new Map<string, string>();
+
+    const translatePath = (path: string, dependencyName: string) => {
+      const cacheKey = `${dependencyName}\0${path}`;
+      const cached = translatePathCache.get(cacheKey);
+      if (cached !== undefined) return cached;
+
+      let result = path;
+      if (path.startsWith(dependencyName)) {
+        const pathParts = splitOutsideParenthesesAndArrays(path);
+        if (pathParts.length > 1) {
+          if (pathParts[1].startsWith('functionCallReturnValue')) {
+            // Check if this function has multiple DIFFERENT type parameters.
+            // If so, DON'T normalize to returnValue - keep the full path to avoid
+            // merging different type-parameterized variants together.
+            const baseName = cleanFunctionName(pathParts[0]);
+            if (!functionsWithMultipleTypeParams.has(baseName)) {
+              // functionCallReturnValue immediately follows - normalize to returnValue
+              result = joinParenthesesAndArrays([
+                'returnValue',
+                ...pathParts.slice(2),
+              ]);
+            }
+          } else if (
+            pathParts[0].endsWith(')') &&
+            pathParts[1].startsWith('signature[')
+          ) {
+            // Hook-style with signature access
+            result = joinParenthesesAndArrays(pathParts.slice(1));
           }
-          // functionCallReturnValue immediately follows - normalize to returnValue
-          // e.g., useAuth().functionCallReturnValue.user -> returnValue.user
-          return joinParenthesesAndArrays([
-            'returnValue',
-            ...pathParts.slice(2),
-          ]);
-        } else if (
-          pathParts[0].endsWith(')') &&
-          pathParts[1].startsWith('signature[')
-        ) {
-          // Hook-style with signature access (e.g., BranchChangesTab().signature[0]...)
-          // Strip the function name for signature equivalency matching
-          return joinParenthesesAndArrays(pathParts.slice(1));
         }
-        // For all other cases (object-style APIs like getSupabase().auth and
-        // direct object references like supabase.from), preserve the path as-is.
-        // The prefix must be kept for proper schema lookups in constructMockCode
-        // and gatherDataForMocks.
       }
-    }
-    return path;
-  };
 
-  const gatherAllEquivalentSchemaPaths = (
-    functionName: string,
-    sourceAndUsageEquivalencies: Pick<
-      DataStructure,
-      'sourceEquivalencies' | 'usageEquivalencies'
-    >,
-    dataStructure?: Pick<
-      DataStructure,
-      'signatureSchema' | 'returnValueSchema'
-    >,
-  ) => {
-    if (!sourceAndUsageEquivalencies) return;
-
-    const findOrCreateEquivalentSchemaPathsEntry = (
-      allPaths: { path: string; functionName?: string }[],
+      translatePathCache.set(cacheKey, result);
+      return result;
+    };
+
+    const gatherAllEquivalentSchemaPaths = (
+      functionName: string,
+      sourceAndUsageEquivalencies: Pick<
+        DataStructure,
+        'sourceEquivalencies' | 'usageEquivalencies'
+      >,
+      dataStructure?: Pick<
+        DataStructure,
+        'signatureSchema' | 'returnValueSchema'
+      >,
     ) => {
-      const equivalentRoots = allPaths
-        .filter(
-          (p) =>
-            p.functionName === rootScopeName ||
-            !!findRelevantDependency(p.functionName),
-        )
-        .map((p) => ({
-          schemaRootPath: p.path,
-          function:
-            p.functionName === rootScopeName
-              ? undefined
-              : findRelevantDependency(p.functionName),
-        }));
-
-      let equivalentSchemaPathsEntry:
-        | (typeof equivalentSchemaPaths)[0]
-        | undefined;
-      for (const pathInfo of allPaths) {
-        if (!equivalentSchemaPathsEntry) {
-          equivalentSchemaPathsEntry = equivalentSchemaPaths.find((esp) =>
-            esp.equivalentRoots.some(
-              (er) =>
-                er.schemaRootPath === pathInfo.path &&
-                (er.function?.name ===
-                  cleanFunctionName(pathInfo.functionName) ||
-                  (!er.function &&
-                    cleanFunctionName(pathInfo.functionName) ===
-                      rootScopeName)),
-            ),
+      checkDeadline();
+      if (!sourceAndUsageEquivalencies) return;
+
+      // Pre-computed normalized schema index cache.
+      // Avoids repeated splitOutsideParenthesesAndArrays calls and function-name
+      // normalization for the same schema paths across multiple equivalency iterations.
+      // The normalization depends on `functionName` (constant per gatherAllEquivalentSchemaPaths call),
+      // so this cache is scoped to this call.
+      type NormalizedEntry = { path: string; parts: string[] };
+      const normalizedSchemaCache = new Map<
+        object,
+        {
+          byFirstPart: Map<string, NormalizedEntry[]>;
+        }
+      >();
+      const getSchemaIndex = (
+        schema: Record<string, string> | undefined,
+      ): { byFirstPart: Map<string, NormalizedEntry[]> } => {
+        if (!schema) return { byFirstPart: new Map() };
+        const cached = normalizedSchemaCache.get(schema);
+        if (cached) return cached;
+        const byFirstPart = new Map<string, NormalizedEntry[]>();
+        for (const path in schema) {
+          checkDeadline();
+          let parts = splitOutsideParenthesesAndArrays(path);
+          if (parts[0].startsWith(functionName)) {
+            const baseName = cleanFunctionName(parts[0]);
+            if (!functionsWithMultipleTypeParams.has(baseName)) {
+              parts =
+                parts[1] === 'functionCallReturnValue'
+                  ? ['returnValue', ...parts.slice(2)]
+                  : parts.slice(1);
+            }
+          }
+          const entry: NormalizedEntry = { path, parts };
+          // Index by the base of the first part (before any function call args)
+          const firstPart = parts[0] ?? '';
+          const parenIdx = firstPart.indexOf('(');
+          const firstPartBase =
+            parenIdx >= 0 ? firstPart.slice(0, parenIdx) : firstPart;
+          let bucket = byFirstPart.get(firstPartBase);
+          if (!bucket) {
+            bucket = [];
+            byFirstPart.set(firstPartBase, bucket);
+          }
+          bucket.push(entry);
+        }
+        const result = { byFirstPart };
+        normalizedSchemaCache.set(schema, result);
+        return result;
+      };
+
+      const findOrCreateEquivalentSchemaPathsEntry = (
+        allPaths: { path: string; functionName?: string }[],
+      ) => {
+        const equivalentRoots = allPaths
+          .filter(
+            (p) =>
+              p.functionName === rootScopeName ||
+              !!findRelevantDependency(p.functionName),
+          )
+          .map((p) => ({
+            schemaRootPath: p.path,
+            function:
+              p.functionName === rootScopeName
+                ? undefined
+                : findRelevantDependency(p.functionName),
+          }));
+
+        let equivalentSchemaPathsEntry:
+          | (typeof equivalentSchemaPaths)[0]
+          | undefined;
+
+        // Collect the signature indices from the new roots we want to add
+        const newRootSignatureIndices = new Set<number>();
+        for (const root of equivalentRoots) {
+          const idx = extractSignatureIndex(root.schemaRootPath);
+          if (idx !== undefined) {
+            newRootSignatureIndices.add(idx);
+          }
+        }
+
+        // Use espIndex Map for O(1) lookup instead of O(E) linear search.
+        // Falls back to linear search only when Map hit has a signature index conflict.
+        for (const pathInfo of allPaths) {
+          checkDeadline();
+          if (equivalentSchemaPathsEntry) break;
+          const candidate = espIndex.get(
+            espIndexKey(pathInfo.path, pathInfo.functionName),
           );
+          if (!candidate) continue;
+
+          // Verify no signature index conflict with the candidate entry
+          if (newRootSignatureIndices.size > 0) {
+            const existingIndicesByFunction = new Map<string, Set<number>>();
+            for (const er of candidate.equivalentRoots) {
+              const funcKey = er.function
+                ? `${er.function.name}::${er.function.filePath}`
+                : '__self__';
+              const idx = extractSignatureIndex(er.schemaRootPath);
+              if (idx !== undefined) {
+                if (!existingIndicesByFunction.has(funcKey)) {
+                  existingIndicesByFunction.set(funcKey, new Set());
+                }
+                existingIndicesByFunction.get(funcKey)!.add(idx);
+              }
+            }
+
+            let hasConflict = false;
+            for (const newRoot of equivalentRoots) {
+              const funcKey = newRoot.function
+                ? `${newRoot.function.name}::${newRoot.function.filePath}`
+                : '__self__';
+              const newIdx = extractSignatureIndex(newRoot.schemaRootPath);
+              if (newIdx !== undefined) {
+                const existingIndices = existingIndicesByFunction.get(funcKey);
+                if (existingIndices && existingIndices.size > 0) {
+                  if (!existingIndices.has(newIdx)) {
+                    hasConflict = true;
+                    break;
+                  }
+                }
+              }
+            }
+
+            if (hasConflict) continue;
+          }
+
+          equivalentSchemaPathsEntry = candidate;
         }
-      }
 
-      if (!equivalentSchemaPathsEntry) {
-        equivalentSchemaPathsEntry = {
-          equivalentRoots,
-          equivalentPostfixes: {},
-        };
-        equivalentSchemaPaths.push(equivalentSchemaPathsEntry);
-      } else {
-        equivalentSchemaPathsEntry.equivalentRoots.push(...equivalentRoots);
-      }
+        if (!equivalentSchemaPathsEntry) {
+          // Before creating a new entry, filter out roots that have conflicting
+          // signature indices from the same function. An entry should never contain
+          // roots with different signature indices from the same function.
+          // This prevents the bug where signature[1], signature[2], signature[4]
+          // all get merged together due to incorrect sourceEquivalencies.
+          let filteredRoots = equivalentRoots;
+          if (newRootSignatureIndices.size > 1) {
+            // There are multiple signature indices - we need to filter to keep only
+            // one consistent set. We'll keep the roots that match the PRIMARY index
+            // (the first signature index we encounter from self, or the lowest index).
+
+            // First, determine the primary index - prefer the self root's index
+            let primaryIndex: number | undefined;
+            for (const root of equivalentRoots) {
+              if (!root.function) {
+                // This is a self root
+                const idx = extractSignatureIndex(root.schemaRootPath);
+                if (idx !== undefined) {
+                  primaryIndex = idx;
+                  break;
+                }
+              }
+            }
+            // If no self root has a signature index, use the lowest index
+            if (primaryIndex === undefined) {
+              primaryIndex = Math.min(...newRootSignatureIndices);
+            }
 
-      // Deduplicate roots using a Set for O(n) instead of O(n²)
-      const seenRoots = new Set<string>();
-      equivalentSchemaPathsEntry.equivalentRoots =
-        equivalentSchemaPathsEntry.equivalentRoots.filter((er) => {
-          const key = er.schemaRootPath + '::' + (er.function?.name ?? '');
-          if (seenRoots.has(key)) return false;
-          seenRoots.add(key);
-          return true;
-        });
+            // Filter roots: keep if no signature index OR signature index matches primary
+            filteredRoots = equivalentRoots.filter((root) => {
+              const idx = extractSignatureIndex(root.schemaRootPath);
+              return idx === undefined || idx === primaryIndex;
+            });
+          }
 
-      return equivalentSchemaPathsEntry;
-    };
+          equivalentSchemaPathsEntry = {
+            equivalentRoots: filteredRoots,
+            equivalentPostfixes: {},
+          };
+          equivalentSchemaPaths.push(equivalentSchemaPathsEntry);
+        } else {
+          equivalentSchemaPathsEntry.equivalentRoots.push(...equivalentRoots);
+        }
 
-    // Helper to extract function name from a path that starts with a function call.
-    // e.g., 'ScenarioViewer().signature[0].scenario' -> 'ScenarioViewer'
-    // Returns undefined if the path doesn't start with a function call or the function isn't a dependency.
-    const extractFunctionNameFromPath = (path: string): string | undefined => {
-      const parts = splitOutsideParenthesesAndArrays(path);
-      if (parts.length > 0 && parts[0].endsWith(')')) {
-        // Extract the function name without the () suffix and type params
-        const funcCallPart = parts[0];
-        const funcName = cleanFunctionName(funcCallPart.replace(/\(\)$/, ''));
-        // Check if this function is a dependency
-        if (findRelevantDependency(funcName)) {
-          return funcName;
+        // Deduplicate roots using a Set for O(n) instead of O(n²)
+        const seenRoots = new Set<string>();
+        equivalentSchemaPathsEntry.equivalentRoots =
+          equivalentSchemaPathsEntry.equivalentRoots.filter((er) => {
+            const key = er.schemaRootPath + '::' + (er.function?.name ?? '');
+            if (seenRoots.has(key)) return false;
+            seenRoots.add(key);
+            return true;
+          });
+
+        // Keep the espIndex in sync after adding/deduplicating roots
+        updateEspIndex(equivalentSchemaPathsEntry);
+
+        return equivalentSchemaPathsEntry;
+      };
+
+      // Helper to extract function name from a path that starts with a function call.
+      // e.g., 'ScenarioViewer().signature[0].scenario' -> 'ScenarioViewer'
+      // Returns undefined if the path doesn't start with a function call or the function isn't a dependency.
+      const extractFunctionNameFromPath = (
+        path: string,
+      ): string | undefined => {
+        const parts = splitOutsideParenthesesAndArrays(path);
+        if (parts.length > 0 && parts[0].endsWith(')')) {
+          // Extract the function name without the () suffix and type params
+          const funcCallPart = parts[0];
+          const funcName = cleanFunctionName(funcCallPart.replace(/\(\)$/, ''));
+          // Check if this function is a dependency
+          if (findRelevantDependency(funcName)) {
+            return funcName;
+          }
         }
-      }
-      return undefined;
-    };
+        return undefined;
+      };
 
-    const allEquivalencies = [
-      sourceAndUsageEquivalencies.usageEquivalencies,
-      sourceAndUsageEquivalencies.sourceEquivalencies,
-    ].filter(Boolean);
-
-    for (const equivalencies of allEquivalencies) {
-      const schemaPathEntries = Object.entries(equivalencies);
-      for (const [schemaPath, usages] of schemaPathEntries) {
-        // First, check if the raw schemaPath starts with a function call to a dependency.
-        // If so, use that dependency name for translation (so translatePath can strip the prefix).
-        const extractedFuncName = extractFunctionNameFromPath(schemaPath);
-        const effectiveFunctionName = extractedFuncName || functionName;
-        const translatedPath = translatePath(schemaPath, effectiveFunctionName);
-
-        const allPaths: { path: string; functionName?: string }[] = [
-          { path: translatedPath, functionName: effectiveFunctionName },
-          ...usages.map((u) => ({
-            path: translatePath(u.schemaPath, u.scopeNodeName),
-            functionName: u.scopeNodeName,
-          })),
-        ].filter((pathInfo) => !pathInfo.path.includes('.map('));
-
-        // Fix 38: Derive base paths from property access paths.
-        // When we have equivalent paths like:
-        //   Parent: signature[0].scenarios[].name
-        //   Child:  signature[0].selectedScenario.name
-        // We want to derive the base paths by finding the common suffix:
-        //   Common suffix: .name
-        //   Parent base: signature[0].scenarios[]
-        //   Child base:  signature[0].selectedScenario
-        // This allows the merge to find nested child schema fields under the base prop.
-
-        // Find child signature paths (paths from child components)
-        const childPaths = allPaths.filter(
-          (p) =>
-            p.functionName &&
-            p.functionName !== rootScopeName &&
-            p.functionName !== effectiveFunctionName,
-        );
-        // Find parent paths (paths from this component)
-        const parentPaths = allPaths.filter(
-          (p) =>
-            !p.functionName ||
-            p.functionName === rootScopeName ||
-            p.functionName === effectiveFunctionName,
-        );
+      const allEquivalencies = [
+        sourceAndUsageEquivalencies.usageEquivalencies,
+        sourceAndUsageEquivalencies.sourceEquivalencies,
+      ].filter(Boolean);
+
+      // Global dedup across ALL equivalency entries. The same (scope, targetPath)
+      // pair often appears in 30-50 different source entries (e.g., every variable
+      // that flows through loadView references the same 50 target paths).
+      // Processing these redundantly accounts for 96% of work in the gather phase.
+      const globalSeenTargets = new Set<string>();
+
+      for (const equivalencies of allEquivalencies) {
+        const schemaPathEntries = Object.entries(equivalencies);
+        for (const [schemaPath, usages] of schemaPathEntries) {
+          checkDeadline();
+
+          // Skip equivalency entries whose source path is a Set/Map membership operation.
+          // Patterns like `.has(articleId)`, `.delete(articleId)`, `.add(articleId)` on
+          // Sets/Maps represent membership checks, not meaningful data flow for schema generation.
+          // In the Margo LibraryPage case, these account for 74% of all equivalency targets
+          // (19,444 of 26,340) and cause a combinatorial explosion in the merge.
+          if (isCollectionMethodPath(schemaPath)) continue;
+
+          // Skip paths with inline object literals in function call arguments.
+          // These are call-site snapshots (e.g., setUndoEntry({ label: '...', undo: ... }))
+          // that embed source code text as path strings. They're expensive to parse
+          // and don't contribute useful schema information.
+          if (hasInlineObjectArg(schemaPath)) continue;
+
+          // First, check if the raw schemaPath starts with a function call to a dependency.
+          // If so, use that dependency name for translation (so translatePath can strip the prefix).
+          const extractedFuncName = extractFunctionNameFromPath(schemaPath);
+          const effectiveFunctionName = extractedFuncName || functionName;
+          const translatedPath = translatePath(
+            schemaPath,
+            effectiveFunctionName,
+          );
 
-        const derivedBasePaths: { path: string; functionName?: string }[] = [];
+          const allPathsRaw: { path: string; functionName?: string }[] = [
+            { path: translatedPath, functionName: effectiveFunctionName },
+            ...usages
+              .filter((u) => !isCollectionMethodPath(u.schemaPath))
+              .map((u) => ({
+                path: translatePath(u.schemaPath, u.scopeNodeName),
+                functionName: u.scopeNodeName,
+              })),
+          ].filter((pathInfo) => !pathInfo.path.includes('.map('));
+
+          // Deduplicate by translated path + function name, both within this entry
+          // AND across all entries. The same target path appears in 30-50 different
+          // source entries (every variable flowing through loadView references the same
+          // 50 target paths). Without global dedup, we process 5,533 targets instead of 217.
+          const allPaths = allPathsRaw.filter((p) => {
+            const key = `${p.functionName ?? ''}::${p.path}`;
+            if (globalSeenTargets.has(key)) return false;
+            globalSeenTargets.add(key);
+            return true;
+          });
 
-        // For each child path, find its equivalent parent path and derive bases
-        for (const childPathInfo of childPaths) {
-          const childParts = splitOutsideParenthesesAndArrays(
-            childPathInfo.path,
+          // Fix 38: Derive base paths from property access paths.
+          // When we have equivalent paths like:
+          //   Parent: signature[0].scenarios[].name
+          //   Child:  signature[0].selectedScenario.name
+          // We want to derive the base paths by finding the common suffix:
+          //   Common suffix: .name
+          //   Parent base: signature[0].scenarios[]
+          //   Child base:  signature[0].selectedScenario
+          // This allows the merge to find nested child schema fields under the base prop.
+
+          // Find child signature paths (paths from child components)
+          const childPaths = allPaths.filter(
+            (p) =>
+              p.functionName &&
+              p.functionName !== rootScopeName &&
+              p.functionName !== effectiveFunctionName,
+          );
+          // Find parent paths (paths from this component)
+          const parentPaths = allPaths.filter(
+            (p) =>
+              !p.functionName ||
+              p.functionName === rootScopeName ||
+              p.functionName === effectiveFunctionName,
           );
 
-          // Look for a parent path that shares a common suffix with this child path
-          for (const parentPathInfo of parentPaths) {
-            const parentParts = splitOutsideParenthesesAndArrays(
-              parentPathInfo.path,
-            );
+          const derivedBasePaths: { path: string; functionName?: string }[] =
+            [];
+          const allPathSet = new Set(allPaths.map((p) => p.path));
+          const derivedBasePathSet = new Set<string>();
 
-            // Find the common suffix (from the end)
-            let commonSuffixLength = 0;
-            const minLen = Math.min(childParts.length, parentParts.length);
-            for (let i = 1; i <= minLen; i++) {
-              if (
-                childParts[childParts.length - i] ===
-                parentParts[parentParts.length - i]
-              ) {
-                commonSuffixLength = i;
-              } else {
-                break;
-              }
-            }
+          // For each child path, find its equivalent parent path and derive bases
+          for (const childPathInfo of childPaths) {
+            checkDeadline();
+            const childParts = splitOutsideParenthesesAndArrays(
+              childPathInfo.path,
+            );
 
-            // If there's a common suffix and both paths have more parts than the suffix
-            if (
-              commonSuffixLength > 0 &&
-              childParts.length > commonSuffixLength &&
-              parentParts.length > commonSuffixLength
-            ) {
-              const childBaseParts = childParts.slice(
-                0,
-                childParts.length - commonSuffixLength,
-              );
-              const parentBaseParts = parentParts.slice(
-                0,
-                parentParts.length - commonSuffixLength,
+            // Look for a parent path that shares a common suffix with this child path
+            for (const parentPathInfo of parentPaths) {
+              const parentParts = splitOutsideParenthesesAndArrays(
+                parentPathInfo.path,
               );
 
-              // Only derive if BOTH paths look like signature paths.
-              // This ensures we're handling JSX child-to-parent prop mappings,
-              // not other complex equivalencies like function call returns.
-              const isChildSignaturePath =
-                childBaseParts[0]?.startsWith('signature[') ||
-                (childBaseParts[0]?.endsWith(')') &&
-                  childBaseParts[1]?.startsWith('signature['));
-              const isParentSignaturePath =
-                parentBaseParts[0]?.startsWith('signature[');
-
-              if (isChildSignaturePath && isParentSignaturePath) {
-                const childBase = joinParenthesesAndArrays(childBaseParts);
-                const parentBase = joinParenthesesAndArrays(parentBaseParts);
-
-                // Only derive if:
-                // 1. Parent has array iteration (e.g., scenarios[]) and child does NOT
-                // 2. Bases are different
-                // 3. Child base is NOT just "signature[N]" (too generic - every component has this)
-                //    We only want specific prop paths like "signature[0].selectedScenario"
-                // This targets array-to-object mappings like scenarios[] -> selectedScenario
-                const parentHasArrayIterator = parentBase.includes('[]');
-                const childHasArrayIterator = childBase.includes('[]');
-
-                // Skip if child base is just the generic signature marker (e.g., "signature[0]")
-                const childBaseIsGenericSignature = /^signature\[\d+\]$/.test(
-                  childBase,
-                );
-
+              // Find the common suffix (from the end)
+              let commonSuffixLength = 0;
+              const minLen = Math.min(childParts.length, parentParts.length);
+              for (let i = 1; i <= minLen; i++) {
                 if (
-                  childBase !== parentBase &&
-                  parentHasArrayIterator &&
-                  !childHasArrayIterator &&
-                  !childBaseIsGenericSignature
+                  childParts[childParts.length - i] ===
+                  parentParts[parentParts.length - i]
                 ) {
-                  // Add child base if not already present
-                  const childBaseExists =
-                    allPaths.some((p) => p.path === childBase) ||
-                    derivedBasePaths.some((p) => p.path === childBase);
-                  if (!childBaseExists) {
-                    derivedBasePaths.push({
-                      path: childBase,
-                      functionName: childPathInfo.functionName,
-                    });
-                  }
+                  commonSuffixLength = i;
+                } else {
+                  break;
+                }
+              }
+
+              // If there's a common suffix and both paths have more parts than the suffix
+              if (
+                commonSuffixLength > 0 &&
+                childParts.length > commonSuffixLength &&
+                parentParts.length > commonSuffixLength
+              ) {
+                const childBaseParts = childParts.slice(
+                  0,
+                  childParts.length - commonSuffixLength,
+                );
+                const parentBaseParts = parentParts.slice(
+                  0,
+                  parentParts.length - commonSuffixLength,
+                );
 
-                  // Add parent base if not already present
-                  const parentBaseExists =
-                    allPaths.some((p) => p.path === parentBase) ||
-                    derivedBasePaths.some((p) => p.path === parentBase);
-                  if (!parentBaseExists) {
-                    derivedBasePaths.push({
-                      path: parentBase,
-                      functionName: parentPathInfo.functionName,
-                    });
+                // Only derive if BOTH paths look like signature paths.
+                // This ensures we're handling JSX child-to-parent prop mappings,
+                // not other complex equivalencies like function call returns.
+                const isChildSignaturePath =
+                  childBaseParts[0]?.startsWith('signature[') ||
+                  (childBaseParts[0]?.endsWith(')') &&
+                    childBaseParts[1]?.startsWith('signature['));
+                const isParentSignaturePath =
+                  parentBaseParts[0]?.startsWith('signature[');
+
+                if (isChildSignaturePath && isParentSignaturePath) {
+                  const childBase = joinParenthesesAndArrays(childBaseParts);
+                  const parentBase = joinParenthesesAndArrays(parentBaseParts);
+
+                  // Only derive if:
+                  // 1. Parent has array iteration (e.g., scenarios[]) and child does NOT
+                  // 2. Bases are different
+                  // 3. Child base is NOT just "signature[N]" (too generic - every component has this)
+                  //    We only want specific prop paths like "signature[0].selectedScenario"
+                  // This targets array-to-object mappings like scenarios[] -> selectedScenario
+                  const parentHasArrayIterator = parentBase.includes('[]');
+                  const childHasArrayIterator = childBase.includes('[]');
+
+                  // Skip if child base is just the generic signature marker (e.g., "signature[0]")
+                  const childBaseIsGenericSignature = /^signature\[\d+\]$/.test(
+                    childBase,
+                  );
+
+                  if (
+                    childBase !== parentBase &&
+                    parentHasArrayIterator &&
+                    !childHasArrayIterator &&
+                    !childBaseIsGenericSignature
+                  ) {
+                    // Add child base if not already present (O(1) Set lookup)
+                    if (
+                      !allPathSet.has(childBase) &&
+                      !derivedBasePathSet.has(childBase)
+                    ) {
+                      derivedBasePaths.push({
+                        path: childBase,
+                        functionName: childPathInfo.functionName,
+                      });
+                      derivedBasePathSet.add(childBase);
+                    }
+
+                    // Add parent base if not already present (O(1) Set lookup)
+                    if (
+                      !allPathSet.has(parentBase) &&
+                      !derivedBasePathSet.has(parentBase)
+                    ) {
+                      derivedBasePaths.push({
+                        path: parentBase,
+                        functionName: parentPathInfo.functionName,
+                      });
+                      derivedBasePathSet.add(parentBase);
+                    }
                   }
                 }
               }
             }
           }
-        }
 
-        allPaths.push(...derivedBasePaths);
-
-        const entry = findOrCreateEquivalentSchemaPathsEntry(allPaths);
-        for (const equivalentRoot of entry.equivalentRoots) {
-          const dataStructures =
-            equivalentRoot.function &&
-            equivalentRoot.function.name !== rootScopeName
-              ? [
-                  findRelevantDependentDataStructure(
-                    equivalentRoot.function.name,
-                  ),
-                  findRelevantDependentAnalysisDataStructure(
-                    equivalentRoot.function.name,
-                  ),
-                ]
-              : [dataStructure];
-
-          // Determine if this is a signature schema path.
-          // The path might be 'signature[0]...' directly, or 'FuncName().signature[0]...' if it has a function prefix.
-          const schemaRootParts = splitOutsideParenthesesAndArrays(
-            equivalentRoot.schemaRootPath,
-          );
-          const isSignaturePath =
-            equivalentRoot.schemaRootPath.startsWith('signature[') ||
-            (schemaRootParts[0]?.endsWith(')') &&
-              schemaRootParts[1]?.startsWith('signature['));
-
-          const schemas = dataStructures.map((dataStructure) =>
-            isSignaturePath
-              ? dataStructure?.signatureSchema
-              : dataStructure?.returnValueSchema,
-          );
-
-          let pathParts = splitOutsideParenthesesAndArrays(
-            equivalentRoot.schemaRootPath,
-          );
-
-          // Fix: When processing a child component's schema, the schemaRootPath has the function
-          // prefix (e.g., 'ScenarioViewer().signature[0].scenario'), but the child's schema paths
-          // don't have that prefix (e.g., 'signature[0].scenario.metadata.screenshotPaths').
-          // Strip the function prefix from pathParts so they can match.
-          if (
-            equivalentRoot.function &&
-            pathParts[0].endsWith(')') &&
-            pathParts[1]?.startsWith('signature[')
-          ) {
-            pathParts = pathParts.slice(1);
+          allPaths.push(...derivedBasePaths);
+
+          const entry = findOrCreateEquivalentSchemaPathsEntry(allPaths);
+
+          // Trace equivalency gathering - helps debug why paths may not be connected
+          if (allPaths.length > 1) {
+            transformationTracer.operation(rootScopeName, {
+              operation: 'gatherEquivalency',
+              stage: 'gathering',
+              path: translatedPath,
+              context: {
+                sourceFunction: functionName,
+                equivalentPaths: allPaths.map((p) => ({
+                  path: p.path,
+                  function: p.functionName,
+                })),
+                equivalentRoots: entry.equivalentRoots.map((r) => ({
+                  path: r.schemaRootPath,
+                  function: r.function?.name,
+                })),
+              },
+            });
           }
+          for (const equivalentRoot of entry.equivalentRoots) {
+            checkDeadline();
+            const dataStructures =
+              equivalentRoot.function &&
+              equivalentRoot.function.name !== rootScopeName
+                ? [
+                    findRelevantDependentDataStructure(
+                      equivalentRoot.function.name,
+                    ),
+                    findRelevantDependentAnalysisDataStructure(
+                      equivalentRoot.function.name,
+                    ),
+                  ]
+                : [dataStructure];
+
+            // Determine if this is a signature schema path.
+            // The path might be 'signature[0]...' directly, or 'FuncName().signature[0]...' if it has a function prefix.
+            const schemaRootParts = splitOutsideParenthesesAndArrays(
+              equivalentRoot.schemaRootPath,
+            );
+            const isSignaturePath =
+              equivalentRoot.schemaRootPath.startsWith('signature[') ||
+              (schemaRootParts[0]?.endsWith(')') &&
+                schemaRootParts[1]?.startsWith('signature['));
+
+            const schemas = dataStructures.map((dataStructure) =>
+              isSignaturePath
+                ? dataStructure?.signatureSchema
+                : dataStructure?.returnValueSchema,
+            );
 
-          for (const schema of schemas) {
-            for (const schemaPath in schema) {
-              let schemaPathParts =
-                splitOutsideParenthesesAndArrays(schemaPath);
-
-              if (schemaPathParts[0].startsWith(functionName)) {
-                // Only normalize if the function doesn't have multiple different type parameters
-                const baseName = cleanFunctionName(schemaPathParts[0]);
-                if (!functionsWithMultipleTypeParams.has(baseName)) {
-                  schemaPathParts =
-                    schemaPathParts[1] === 'functionCallReturnValue'
-                      ? ['returnValue', ...schemaPathParts.slice(2)]
-                      : schemaPathParts.slice(1);
-                }
-              }
+            let pathParts = splitOutsideParenthesesAndArrays(
+              equivalentRoot.schemaRootPath,
+            );
 
-              if (schemaPathParts.length < pathParts.length) continue;
+            // Fix: When processing a child component's schema, the schemaRootPath has the function
+            // prefix (e.g., 'ScenarioViewer().signature[0].scenario'), but the child's schema paths
+            // don't have that prefix (e.g., 'signature[0].scenario.metadata.screenshotPaths').
+            // Strip the function prefix from pathParts so they can match.
+            if (
+              equivalentRoot.function &&
+              pathParts[0].endsWith(')') &&
+              pathParts[1]?.startsWith('signature[')
+            ) {
+              pathParts = pathParts.slice(1);
+            }
 
-              // Check if all path parts match (allowing function call variants)
-              let allMatch = true;
-              let matchedUpToIndex = pathParts.length;
-              for (let i = 0; i < pathParts.length; i++) {
-                if (!pathPartMatches(pathParts[i], schemaPathParts[i])) {
-                  allMatch = false;
-                  break;
-                }
-                // If the last pathPart matched a function call variant,
-                // we need to include it in the postfix calculation
-                if (
-                  i === pathParts.length - 1 &&
-                  schemaPathParts[i] !== pathParts[i] &&
-                  schemaPathParts[i].startsWith(pathParts[i] + '(')
-                ) {
-                  // The schemaPathPart is a function call variant (e.g., 'isEntityBeingAnalyzed(entity.sha)')
-                  // We want to include this as part of the postfix
-                  matchedUpToIndex = i;
+            for (const schema of schemas) {
+              // Use pre-computed index to only iterate schema entries whose
+              // normalized first part matches pathParts[0], instead of all entries.
+              const schemaIndex = getSchemaIndex(schema);
+              const lookupPart = pathParts[0] ?? '';
+              const lookupParenIdx = lookupPart.indexOf('(');
+              const lookupBase =
+                lookupParenIdx >= 0
+                  ? lookupPart.slice(0, lookupParenIdx)
+                  : lookupPart;
+              const candidates = schemaIndex.byFirstPart.get(lookupBase) || [];
+              for (const {
+                path: schemaPath,
+                parts: schemaPathParts,
+              } of candidates) {
+                checkDeadline();
+                if (schemaPathParts.length < pathParts.length) continue;
+
+                // Check if all path parts match (allowing function call variants)
+                let allMatch = true;
+                let matchedUpToIndex = pathParts.length;
+                for (let i = 0; i < pathParts.length; i++) {
+                  if (!pathPartMatches(pathParts[i], schemaPathParts[i])) {
+                    allMatch = false;
+                    break;
+                  }
+                  // If the last pathPart matched a function call variant,
+                  // we need to include it in the postfix calculation
+                  if (
+                    i === pathParts.length - 1 &&
+                    schemaPathParts[i] !== pathParts[i] &&
+                    schemaPathParts[i].startsWith(pathParts[i] + '(')
+                  ) {
+                    // The schemaPathPart is a function call variant (e.g., 'isEntityBeingAnalyzed(entity.sha)')
+                    // We want to include this as part of the postfix
+                    matchedUpToIndex = i;
+                  }
                 }
-              }
 
-              if (allMatch) {
-                // When we matched a function call variant at the end (e.g., 'foo' matched 'foo(args)'),
-                // the base itself should be marked as a function, and the function call details
-                // should be included as sub-paths
-                if (matchedUpToIndex < pathParts.length) {
-                  // This is a function call variant match at the last position
-                  // Mark the base as a function (empty postfix = the base path itself)
-                  entry.equivalentPostfixes[''] = bestValueFromOptions([
-                    entry.equivalentPostfixes[''],
-                    'function',
-                  ]);
-
-                  // Also capture the function call and any remaining parts
-                  // e.g., 'isEntityBeingAnalyzed(entity.sha)' or 'isEntityBeingAnalyzed(entity.sha).functionCallReturnValue'
-                  const funcCallPart = schemaPathParts[matchedUpToIndex];
-                  const baseName = pathParts[matchedUpToIndex]; // e.g., 'isEntityBeingAnalyzed'
-                  const argsMatch = funcCallPart.match(/\(.*\)$/);
-
-                  if (argsMatch) {
-                    // Create postfix using just the args portion: (entity.sha) instead of isEntityBeingAnalyzed(entity.sha)
-                    // This avoids duplicating the base name in the final path
-                    const argsPortion = argsMatch[0]; // e.g., '(entity.sha)'
-                    const remainingParts = schemaPathParts.slice(
-                      matchedUpToIndex + 1,
+                if (allMatch) {
+                  // When we matched a function call variant at the end (e.g., 'foo' matched 'foo(args)'),
+                  // the base itself should be marked as a function, and the function call details
+                  // should be included as sub-paths
+                  if (matchedUpToIndex < pathParts.length) {
+                    // This is a function call variant match at the last position
+                    // Mark the base as a function (empty postfix = the base path itself)
+                    entry.equivalentPostfixes[''] = bestValueFromOptions([
+                      entry.equivalentPostfixes[''],
+                      'function',
+                    ]);
+
+                    // Also capture the function call and any remaining parts
+                    // e.g., 'isEntityBeingAnalyzed(entity.sha)' or 'isEntityBeingAnalyzed(entity.sha).functionCallReturnValue'
+                    const funcCallPart = schemaPathParts[matchedUpToIndex];
+                    const baseName = pathParts[matchedUpToIndex]; // e.g., 'isEntityBeingAnalyzed'
+                    const argsMatch = funcCallPart.match(/\(.*\)$/);
+
+                    if (argsMatch) {
+                      // Create postfix using just the args portion: (entity.sha) instead of isEntityBeingAnalyzed(entity.sha)
+                      // This avoids duplicating the base name in the final path
+                      const argsPortion = argsMatch[0]; // e.g., '(entity.sha)'
+                      const remainingParts = schemaPathParts.slice(
+                        matchedUpToIndex + 1,
+                      );
+
+                      // Build the postfix as: (args).remaining.parts
+                      const funcPostfix = joinParenthesesAndArrays([
+                        argsPortion,
+                        ...remainingParts,
+                      ]);
+                      entry.equivalentPostfixes[funcPostfix] = entry
+                        .equivalentPostfixes[funcPostfix]
+                        ? bestValueFromOptions([
+                            entry.equivalentPostfixes[funcPostfix],
+                            schema[schemaPath],
+                          ])
+                        : schema[schemaPath];
+                    }
+                  } else {
+                    // Regular exact match - use the standard postfix logic
+                    const postfix = joinParenthesesAndArrays(
+                      schemaPathParts.slice(matchedUpToIndex),
                     );
 
-                    // Build the postfix as: (args).remaining.parts
-                    const funcPostfix = joinParenthesesAndArrays([
-                      argsPortion,
-                      ...remainingParts,
-                    ]);
-                    entry.equivalentPostfixes[funcPostfix] = entry
-                      .equivalentPostfixes[funcPostfix]
-                      ? bestValueFromOptions([
-                          entry.equivalentPostfixes[funcPostfix],
-                          schema[schemaPath],
-                        ])
-                      : schema[schemaPath];
+                    const previousValue = entry.equivalentPostfixes[postfix];
+                    const newValue = schema[schemaPath];
+                    entry.equivalentPostfixes[postfix] = previousValue
+                      ? bestValueFromOptions([previousValue, newValue])
+                      : newValue;
+
+                    // Trace postfix gathering - shows where type info comes from
+                    if (entry.equivalentPostfixes[postfix] !== previousValue) {
+                      transformationTracer.operation(rootScopeName, {
+                        operation: 'gatherPostfix',
+                        stage: 'gathering',
+                        path: postfix || '(root)',
+                        before: previousValue,
+                        after: entry.equivalentPostfixes[postfix],
+                        context: {
+                          sourceSchemaPath: schemaPath,
+                          sourceFunction:
+                            equivalentRoot.function?.name || rootScopeName,
+                          equivalentRootPath: equivalentRoot.schemaRootPath,
+                          rawValue: newValue,
+                        },
+                      });
+                    }
                   }
-                } else {
-                  // Regular exact match - use the standard postfix logic
-                  const postfix = joinParenthesesAndArrays(
-                    schemaPathParts.slice(matchedUpToIndex),
-                  );
-
-                  entry.equivalentPostfixes[postfix] = entry
-                    .equivalentPostfixes[postfix]
-                    ? bestValueFromOptions([
-                        entry.equivalentPostfixes[postfix],
-                        schema[schemaPath],
-                      ])
-                    : schema[schemaPath];
                 }
               }
             }
           }
         }
       }
-    }
 
-    if (Object.keys(dataStructure?.returnValueSchema ?? {}).length > 0) {
-      // Find all paths that contain functionCallReturnValue and extract unique base paths
-      // For each path containing functionCallReturnValue, find the FIRST occurrence and use
-      // that as a base path. This handles nested cases like:
-      //   X().functionCallReturnValue.A.B.Y().functionCallReturnValue
-      // where we want both X().functionCallReturnValue and Y().functionCallReturnValue as bases
-      const allBasePaths = new Set<string>();
-      for (const path of Object.keys(dataStructure.returnValueSchema)) {
-        const parts = splitOutsideParenthesesAndArrays(path);
-        // Find all positions of functionCallReturnValue and create base paths for each
-        for (let i = 0; i < parts.length; i++) {
-          if (parts[i] === 'functionCallReturnValue') {
-            const basePath = joinParenthesesAndArrays(parts.slice(0, i + 1));
-            allBasePaths.add(basePath);
+      if (Object.keys(dataStructure?.returnValueSchema ?? {}).length > 0) {
+        // Find all paths that contain functionCallReturnValue and extract unique base paths
+        // For each path containing functionCallReturnValue, find the FIRST occurrence and use
+        // that as a base path. This handles nested cases like:
+        //   X().functionCallReturnValue.A.B.Y().functionCallReturnValue
+        // where we want both X().functionCallReturnValue and Y().functionCallReturnValue as bases
+        const allBasePaths = new Set<string>();
+        for (const path of Object.keys(dataStructure.returnValueSchema)) {
+          checkDeadline();
+          const parts = splitOutsideParenthesesAndArrays(path);
+          // Find all positions of functionCallReturnValue and create base paths for each
+          for (let i = 0; i < parts.length; i++) {
+            if (parts[i] === 'functionCallReturnValue') {
+              const basePath = joinParenthesesAndArrays(parts.slice(0, i + 1));
+              allBasePaths.add(basePath);
+            }
           }
         }
-      }
 
-      // Sort by length so shorter paths are processed first
-      const sortedBasePaths = [...allBasePaths].sort(
-        (a, b) => a.length - b.length,
-      );
+        // Sort by length so shorter paths are processed first
+        const sortedBasePaths = [...allBasePaths].sort(
+          (a, b) => a.length - b.length,
+        );
 
-      for (const basePath of sortedBasePaths) {
-        const translatedBasePath = translatePath(basePath, functionName);
-        const entry = findOrCreateEquivalentSchemaPathsEntry([
-          { path: translatedBasePath, functionName: functionName },
-        ]);
-        entry.equivalentRoots.push({
-          schemaRootPath: translatedBasePath,
-          function: findRelevantDependency(functionName),
-        });
+        for (const basePath of sortedBasePaths) {
+          const translatedBasePath = translatePath(basePath, functionName);
+          const entry = findOrCreateEquivalentSchemaPathsEntry([
+            { path: translatedBasePath, functionName: functionName },
+          ]);
+          const newRoot = {
+            schemaRootPath: translatedBasePath,
+            function: findRelevantDependency(functionName),
+          };
+          entry.equivalentRoots.push(newRoot);
+          // Update index for the newly added root
+          const newRootFuncName = newRoot.function?.name ?? rootScopeName;
+          espIndex.set(
+            espIndexKey(newRoot.schemaRootPath, newRootFuncName),
+            entry,
+          );
 
-        const basePathParts = splitOutsideParenthesesAndArrays(basePath);
-        for (const schemaPath in dataStructure.returnValueSchema) {
-          const schemaPathParts = splitOutsideParenthesesAndArrays(schemaPath);
-          if (schemaPathParts.length < basePathParts.length) continue;
+          const basePathParts = splitOutsideParenthesesAndArrays(basePath);
+          for (const schemaPath in dataStructure.returnValueSchema) {
+            checkDeadline();
+            const schemaPathParts =
+              splitOutsideParenthesesAndArrays(schemaPath);
+            if (schemaPathParts.length < basePathParts.length) continue;
 
-          // Check if this schemaPath actually starts with this basePath
-          // (not just has the same length prefix)
-          const prefixParts = schemaPathParts.slice(0, basePathParts.length);
-          if (
-            joinParenthesesAndArrays(prefixParts) !==
-            joinParenthesesAndArrays(basePathParts)
-          ) {
-            continue;
-          }
+            // Check if this schemaPath actually starts with this basePath
+            // (not just has the same length prefix)
+            const prefixParts = schemaPathParts.slice(0, basePathParts.length);
+            if (
+              joinParenthesesAndArrays(prefixParts) !==
+              joinParenthesesAndArrays(basePathParts)
+            ) {
+              continue;
+            }
 
-          const postfix = joinParenthesesAndArrays(
-            schemaPathParts.slice(basePathParts.length),
-          );
-          entry.equivalentPostfixes[postfix] = entry.equivalentPostfixes[
-            postfix
-          ]
-            ? bestValueFromOptions([
-                entry.equivalentPostfixes[postfix],
-                dataStructure.returnValueSchema[schemaPath],
-              ])
-            : dataStructure.returnValueSchema[schemaPath];
+            const postfix = joinParenthesesAndArrays(
+              schemaPathParts.slice(basePathParts.length),
+            );
+            const newValue = entry.equivalentPostfixes[postfix]
+              ? bestValueFromOptions([
+                  entry.equivalentPostfixes[postfix],
+                  dataStructure.returnValueSchema[schemaPath],
+                ])
+              : dataStructure.returnValueSchema[schemaPath];
+
+            entry.equivalentPostfixes[postfix] = newValue;
+          }
         }
       }
-    }
-  };
-
-  const mergeAllEquivalentSchemaPaths = () => {
-    const mergedEquivalentSchemaPaths: typeof equivalentSchemaPaths = [];
+    };
 
-    // Pre-pass: Connect entries with array/array-element relationships.
-    // This handles cases like:
-    // - Entry A has root 'surveys' (array)
-    // - Entry B has root 'surveys[]' (array element)
-    // These need to be connected so Entry B's field postfixes flow to Entry A.
-    // We do this before the main merge to ensure the connection happens regardless
-    // of processing order.
-    for (const esp of equivalentSchemaPaths) {
-      for (const root of esp.equivalentRoots) {
-        if (root.schemaRootPath.endsWith('[]')) {
-          // Find a matching parent entry with the base array path
-          const baseArrayPath = root.schemaRootPath.slice(0, -2);
-          const parentEntry = equivalentSchemaPaths.find(
-            (other) =>
-              other !== esp &&
-              other.equivalentRoots.some(
-                (otherRoot) =>
-                  otherRoot.schemaRootPath === baseArrayPath &&
-                  otherRoot.function?.name === root.function?.name &&
-                  otherRoot.function?.filePath === root.function?.filePath,
-              ),
-          );
-          if (parentEntry) {
-            // Add transformed postfixes from child (array element) to parent (array)
-            // so they can be applied with [] prefix to parent paths
-            for (const [postfixPath, postfixValue] of Object.entries(
-              esp.equivalentPostfixes,
-            )) {
-              const transformedPostfix = joinParenthesesAndArrays(
-                ['[]', postfixPath].filter(Boolean),
-              );
-              if (!(transformedPostfix in parentEntry.equivalentPostfixes)) {
-                parentEntry.equivalentPostfixes[transformedPostfix] =
-                  postfixValue;
+    const mergeAllEquivalentSchemaPaths = () => {
+      const mergedEquivalentSchemaPaths: typeof equivalentSchemaPaths = [];
+
+      // Pre-pass: Connect entries with array/array-element relationships.
+      // This handles cases like:
+      // - Entry A has root 'surveys' (array)
+      // - Entry B has root 'surveys[]' (array element)
+      // These need to be connected so Entry B's field postfixes flow to Entry A.
+      // We do this before the main merge to ensure the connection happens regardless
+      // of processing order.
+      for (const esp of equivalentSchemaPaths) {
+        checkDeadline();
+        for (const root of esp.equivalentRoots) {
+          if (root.schemaRootPath.endsWith('[]')) {
+            // Find a matching parent entry with the base array path
+            const baseArrayPath = root.schemaRootPath.slice(0, -2);
+            const parentEntry = equivalentSchemaPaths.find(
+              (other) =>
+                other !== esp &&
+                other.equivalentRoots.some(
+                  (otherRoot) =>
+                    otherRoot.schemaRootPath === baseArrayPath &&
+                    otherRoot.function?.name === root.function?.name &&
+                    otherRoot.function?.filePath === root.function?.filePath,
+                ),
+            );
+            if (parentEntry) {
+              // Add transformed postfixes from child (array element) to parent (array)
+              // so they can be applied with [] prefix to parent paths
+              for (const [postfixPath, postfixValue] of Object.entries(
+                esp.equivalentPostfixes,
+              )) {
+                checkDeadline();
+                const transformedPostfix = joinParenthesesAndArrays(
+                  ['[]', postfixPath].filter(Boolean),
+                );
+                if (!(transformedPostfix in parentEntry.equivalentPostfixes)) {
+                  parentEntry.equivalentPostfixes[transformedPostfix] =
+                    postfixValue;
+                }
               }
             }
           }
         }
       }
-    }
 
-    const findEquivalentSchemaPathEntry = (
-      schemaSubPath: string,
-      equivalentRootFunction: (typeof equivalentSchemaPaths)[0]['equivalentRoots'][0]['function'],
-    ) => {
-      let postfix: string | undefined;
-      const equivalentEntry = mergedEquivalentSchemaPaths.find((esp) =>
-        esp.equivalentRoots.some((er) => {
-          if (
-            (schemaSubPath.startsWith('returnValue') ||
-              schemaSubPath.startsWith('signature[')) &&
-            (er.function?.name !== equivalentRootFunction?.name ||
-              er.function?.filePath !== equivalentRootFunction?.filePath)
-          ) {
-            return false;
-          }
+      const findEquivalentSchemaPathEntry = (
+        schemaSubPath: string,
+        equivalentRootFunction: (typeof equivalentSchemaPaths)[0]['equivalentRoots'][0]['function'],
+      ) => {
+        let postfix: string | undefined;
 
-          if (schemaSubPath === er.schemaRootPath) {
-            postfix = er.postfix;
-            return true;
-          }
+        // Get the signature index we're looking for (if any)
+        const lookingForSignatureIndex = extractSignatureIndex(schemaSubPath);
 
-          return false;
-        }),
-      );
+        const equivalentEntry = mergedEquivalentSchemaPaths.find((esp) =>
+          esp.equivalentRoots.some((er) => {
+            if (
+              (schemaSubPath.startsWith('returnValue') ||
+                schemaSubPath.startsWith('signature[')) &&
+              (er.function?.name !== equivalentRootFunction?.name ||
+                er.function?.filePath !== equivalentRootFunction?.filePath)
+            ) {
+              return false;
+            }
 
-      return { equivalentEntry, postfix };
-    };
+            if (schemaSubPath === er.schemaRootPath) {
+              // Additional check: if we're looking for a signature path, make sure
+              // the entry doesn't already have DIFFERENT signature indices.
+              // This prevents entries with signature[1], signature[2], signature[4]
+              // from all being merged together.
+              if (lookingForSignatureIndex !== undefined) {
+                const hasConflictingSignatureIndex = esp.equivalentRoots.some(
+                  (otherRoot) => {
+                    // Only check roots from the same function
+                    if (
+                      otherRoot.function?.name !==
+                        equivalentRootFunction?.name ||
+                      otherRoot.function?.filePath !==
+                        equivalentRootFunction?.filePath
+                    ) {
+                      return false;
+                    }
+                    const otherIndex = extractSignatureIndex(
+                      otherRoot.schemaRootPath,
+                    );
+                    return (
+                      otherIndex !== undefined &&
+                      otherIndex !== lookingForSignatureIndex
+                    );
+                  },
+                );
+                if (hasConflictingSignatureIndex) {
+                  return false;
+                }
+              }
 
-    const sortedEquivalentSchemaPaths = equivalentSchemaPaths.sort(
-      (a, b) =>
-        Math.max(
-          ...a.equivalentRoots.map(
-            (er) => splitOutsideParenthesesAndArrays(er.schemaRootPath).length,
-          ),
-        ) -
-        Math.max(
-          ...b.equivalentRoots.map(
-            (er) => splitOutsideParenthesesAndArrays(er.schemaRootPath).length,
-          ),
-        ),
-    );
+              postfix = er.postfix;
+              return true;
+            }
 
-    for (const esp of sortedEquivalentSchemaPaths) {
-      if (esp.equivalentRoots.length === 0) continue;
-      let bestCandidateLength: number | undefined;
-      let bestCandidate: (typeof equivalentSchemaPaths)[0] | undefined;
-      let postfix: string | undefined;
-      for (const equivalentRoot of esp.equivalentRoots) {
-        const rootSchemaPath = equivalentRoot.schemaRootPath;
-        const schemaPathParts =
-          splitOutsideParenthesesAndArrays(rootSchemaPath);
-
-        for (let i = 0; i < schemaPathParts.length; i++) {
-          const subPath = joinParenthesesAndArrays(
-            schemaPathParts.slice(0, i + 1),
-          );
+            return false;
+          }),
+        );
 
-          const { equivalentEntry, postfix: equivalentEntryPostfix } =
-            findEquivalentSchemaPathEntry(subPath, equivalentRoot.function);
-          if (
-            equivalentEntry &&
-            (!bestCandidateLength || bestCandidateLength > i + 1)
-          ) {
-            bestCandidate = equivalentEntry;
-            bestCandidateLength = i + 1;
-            postfix = joinParenthesesAndArrays(
-              [equivalentEntryPostfix, ...schemaPathParts.slice(i + 1)].filter(
-                Boolean,
-              ),
+        return { equivalentEntry, postfix };
+      };
+
+      const sortedEquivalentSchemaPaths = equivalentSchemaPaths.sort(
+        (a, b) =>
+          Math.max(
+            ...a.equivalentRoots.map(
+              (er) =>
+                splitOutsideParenthesesAndArrays(er.schemaRootPath).length,
+            ),
+          ) -
+          Math.max(
+            ...b.equivalentRoots.map(
+              (er) =>
+                splitOutsideParenthesesAndArrays(er.schemaRootPath).length,
+            ),
+          ),
+      );
+
+      for (const esp of sortedEquivalentSchemaPaths) {
+        checkDeadline();
+        if (esp.equivalentRoots.length === 0) continue;
+        let bestCandidateLength: number | undefined;
+        let bestCandidate: (typeof equivalentSchemaPaths)[0] | undefined;
+        let postfix: string | undefined;
+        for (const equivalentRoot of esp.equivalentRoots) {
+          const rootSchemaPath = equivalentRoot.schemaRootPath;
+          const schemaPathParts =
+            splitOutsideParenthesesAndArrays(rootSchemaPath);
+
+          for (let i = 0; i < schemaPathParts.length; i++) {
+            const subPath = joinParenthesesAndArrays(
+              schemaPathParts.slice(0, i + 1),
             );
+
+            const { equivalentEntry, postfix: equivalentEntryPostfix } =
+              findEquivalentSchemaPathEntry(subPath, equivalentRoot.function);
+            if (
+              equivalentEntry &&
+              (!bestCandidateLength || bestCandidateLength > i + 1)
+            ) {
+              bestCandidate = equivalentEntry;
+              bestCandidateLength = i + 1;
+              postfix = joinParenthesesAndArrays(
+                [
+                  equivalentEntryPostfix,
+                  ...schemaPathParts.slice(i + 1),
+                ].filter(Boolean),
+              );
+            }
           }
         }
-      }
 
-      if (bestCandidate) {
-        for (const root of esp.equivalentRoots) {
-          if (postfix.length > 0) {
-            root.postfix = postfix;
+        if (bestCandidate) {
+          for (const root of esp.equivalentRoots) {
+            if (postfix.length > 0) {
+              root.postfix = postfix;
+            }
+
+            bestCandidate.equivalentRoots.push(root);
           }
 
-          bestCandidate.equivalentRoots.push(root);
+          const postfixesToMerge =
+            postfix.length > 0
+              ? Object.keys(esp.equivalentPostfixes).reduce(
+                  (acc, postfixPath) => {
+                    const fullPath = joinParenthesesAndArrays([
+                      postfix,
+                      postfixPath,
+                    ]);
+                    acc[fullPath] = esp.equivalentPostfixes[postfixPath];
+                    return acc;
+                  },
+                  {} as Record<string, string>,
+                )
+              : esp.equivalentPostfixes;
+
+          bestCandidate.equivalentPostfixes = {
+            ...bestCandidate.equivalentPostfixes,
+            ...postfixesToMerge,
+          };
+        } else {
+          mergedEquivalentSchemaPaths.push(esp);
         }
+      }
 
-        const postfixesToMerge =
-          postfix.length > 0
-            ? Object.keys(esp.equivalentPostfixes).reduce(
-                (acc, postfixPath) => {
-                  const fullPath = joinParenthesesAndArrays([
-                    postfix,
-                    postfixPath,
-                  ]);
-                  acc[fullPath] = esp.equivalentPostfixes[postfixPath];
-                  return acc;
-                },
-                {} as Record<string, string>,
-              )
-            : esp.equivalentPostfixes;
+      return mergedEquivalentSchemaPaths;
+    };
 
-        bestCandidate.equivalentPostfixes = {
-          ...bestCandidate.equivalentPostfixes,
-          ...postfixesToMerge,
-        };
-      } else {
-        mergedEquivalentSchemaPaths.push(esp);
+    // Build a lookup of mocked dependencies to skip their internal implementation
+    const mockedDependencies = new Set<string>();
+    for (const dep of importedExports) {
+      if (dep.isMocked) {
+        mockedDependencies.add(`${dep.filePath}::${dep.name}`);
       }
     }
 
-    return mergedEquivalentSchemaPaths;
-  };
-
-  // Build a lookup of mocked dependencies to skip their internal implementation
-  const mockedDependencies = new Set<string>();
-  for (const dep of importedExports) {
-    if (dep.isMocked) {
-      mockedDependencies.add(`${dep.filePath}::${dep.name}`);
+    gatherAllEquivalentSchemaPaths(rootScopeName, dataStructure);
+
+    // Process dependencySchemas for all dependencies (including mocked ones)
+    // dependencySchemas contains usage information (how dependencies are called),
+    // not internal implementation, so we want this for mocked dependencies too
+    for (const dependency of importedExports) {
+      checkDeadline();
+      const dependentDataStructure =
+        dependencySchemas?.[dependency.filePath]?.[dependency.name];
+      if (!dependentDataStructure) continue;
+      gatherAllEquivalentSchemaPaths(
+        dependency.name,
+        dependentDataStructure,
+        dependentDataStructure,
+      );
     }
-  }
 
-  gatherAllEquivalentSchemaPaths(rootScopeName, dataStructure);
-
-  // Process dependencySchemas for all dependencies (including mocked ones)
-  // dependencySchemas contains usage information (how dependencies are called),
-  // not internal implementation, so we want this for mocked dependencies too
-  for (const dependency of importedExports) {
-    const dependentDataStructure =
-      dependencySchemas?.[dependency.filePath]?.[dependency.name];
-    if (!dependentDataStructure) continue;
-    gatherAllEquivalentSchemaPaths(
-      dependency.name,
-      dependentDataStructure,
-      dependentDataStructure,
-    );
-  }
-
-  for (const filePath in dependentAnalyses) {
-    for (const name in dependentAnalyses[filePath]) {
-      // Skip mocked dependencies - we don't want to merge in their internal implementation
-      if (mockedDependencies.has(`${filePath}::${name}`)) {
-        continue;
-      }
+    for (const filePath in dependentAnalyses) {
+      for (const name in dependentAnalyses[filePath]) {
+        // Skip mocked dependencies - we don't want to merge in their internal implementation
+        if (mockedDependencies.has(`${filePath}::${name}`)) {
+          continue;
+        }
 
-      const childMergedDataStructure =
-        dependentAnalyses[filePath][name].metadata?.mergedDataStructure || {};
+        const childMergedDataStructure =
+          dependentAnalyses[filePath][name].metadata?.mergedDataStructure || {};
 
-      gatherAllEquivalentSchemaPaths(name, childMergedDataStructure as any);
+        gatherAllEquivalentSchemaPaths(name, childMergedDataStructure as any);
+      }
     }
-  }
 
-  equivalentSchemaPaths = mergeAllEquivalentSchemaPaths();
+    const gatherElapsed = Date.now() - mergeStartTime;
 
-  for (const esp of equivalentSchemaPaths) {
-    // Pre-compute which postfixes have children to avoid O(n²) lookups in the inner loop.
-    // A postfix "has children" if there are other postfixes that extend it.
-    const postfixesWithChildren = new Set<string>();
-    const postfixKeys = Object.keys(esp.equivalentPostfixes);
+    equivalentSchemaPaths = mergeAllEquivalentSchemaPaths();
 
-    // Check for empty postfix having children (any other postfixes exist)
-    if (postfixKeys.length > 1 && '' in esp.equivalentPostfixes) {
-      postfixesWithChildren.add('');
-    }
+    const mergeEspElapsed = Date.now() - mergeStartTime;
 
-    // Check for array element postfixes having children using a prefix set.
-    // This avoids O(n²) scans across large postfix lists.
-    // e.g., 'currentEntities[]' has children if a path like 'currentEntities[].sha' exists.
-    const postfixPrefixSet = new Set<string>();
-    for (const postfixPath of postfixKeys) {
-      if (!postfixPath) continue;
-      const parts = splitOutsideParenthesesAndArrays(postfixPath);
-      for (let i = 1; i < parts.length; i++) {
-        postfixPrefixSet.add(joinParenthesesAndArrays(parts.slice(0, i)));
-      }
-    }
-    for (const postfixPath of postfixKeys) {
-      if (postfixPath.endsWith('[]') && postfixPrefixSet.has(postfixPath)) {
-        postfixesWithChildren.add(postfixPath);
-      }
-    }
+    // Collect schemas that need cleaning — batch the calls for the end instead of
+    // calling cleanSchema inside the inner root loop (which was O(roots * schemaSize)).
+    const schemasToClean = new Set<{ [key: string]: string }>();
 
-    // Deduplicate equivalentRoots that would write to the same schema paths.
-    // Roots with the same (function, schemaRootPath, postfix) are redundant.
-    const seenRootKeys = new Set<string>();
-    const uniqueRoots = esp.equivalentRoots.filter((root) => {
-      const key = `${root.function?.filePath ?? ''}::${root.function?.name ?? ''}::${root.schemaRootPath}::${root.postfix ?? ''}`;
-      if (seenRootKeys.has(key)) return false;
-      seenRootKeys.add(key);
-      return true;
-    });
+    for (const esp of equivalentSchemaPaths) {
+      checkDeadline();
+      // Pre-compute which postfixes have children to avoid O(n²) lookups in the inner loop.
+      // A postfix "has children" if there are other postfixes that extend it.
+      const postfixesWithChildren = new Set<string>();
+      const postfixKeys = Object.keys(esp.equivalentPostfixes);
+
+      // Pre-parse ALL postfix paths once. These parsed parts are reused in:
+      // 1. The children detection loop below
+      // 2. The inner postfix application loop (lines that split postfixPath and equivalentRoot.postfix)
+      // This eliminates thousands of redundant splitOutsideParenthesesAndArrays calls.
+      const postfixPartsCache = new Map<string, string[]>();
+      for (const postfixPath of postfixKeys) {
+        if (!postfixPath) continue;
+        postfixPartsCache.set(
+          postfixPath,
+          splitOutsideParenthesesAndArrays(postfixPath),
+        );
+      }
 
-    for (const equivalentRoot of uniqueRoots) {
-      let merged:
-        | {
-            signatureSchema: { [key: string]: string };
-            returnValueSchema: { [key: string]: string };
-          }
-        | undefined;
+      // Check for empty postfix having children (any other postfixes exist)
+      if (postfixKeys.length > 1 && '' in esp.equivalentPostfixes) {
+        postfixesWithChildren.add('');
+      }
 
-      if (equivalentRoot.function) {
-        merged = findOrCreateDependentSchemas(equivalentRoot.function);
-      } else {
-        merged = mergedDataStructure;
+      // Check for array element postfixes having children using a prefix set.
+      // This avoids O(n²) scans across large postfix lists.
+      // e.g., 'currentEntities[]' has children if a path like 'currentEntities[].sha' exists.
+      const postfixPrefixSet = new Set<string>();
+      for (const postfixPath of postfixKeys) {
+        if (!postfixPath) continue;
+        const parts = postfixPartsCache.get(postfixPath)!;
+        for (let i = 1; i < parts.length; i++) {
+          postfixPrefixSet.add(joinParenthesesAndArrays(parts.slice(0, i)));
+        }
+      }
+      for (const postfixPath of postfixKeys) {
+        if (postfixPath.endsWith('[]') && postfixPrefixSet.has(postfixPath)) {
+          postfixesWithChildren.add(postfixPath);
+        }
       }
 
-      if (!merged) continue;
+      // Deduplicate equivalentRoots that would write to the same schema paths.
+      // Roots with the same (function, schemaRootPath, postfix) are redundant.
+      const seenRootKeys = new Set<string>();
+      const uniqueRoots = esp.equivalentRoots.filter((root) => {
+        const key = `${root.function?.filePath ?? ''}::${root.function?.name ?? ''}::${root.schemaRootPath}::${root.postfix ?? ''}`;
+        if (seenRootKeys.has(key)) return false;
+        seenRootKeys.add(key);
+        return true;
+      });
+
+      for (const equivalentRoot of uniqueRoots) {
+        checkDeadline();
+        let merged:
+          | {
+              signatureSchema: { [key: string]: string };
+              returnValueSchema: { [key: string]: string };
+            }
+          | undefined;
 
-      const schema = equivalentRoot.schemaRootPath.startsWith('signature[')
-        ? merged.signatureSchema
-        : merged.returnValueSchema;
+        if (equivalentRoot.function) {
+          merged = findOrCreateDependentSchemas(equivalentRoot.function);
+        } else {
+          merged = mergedDataStructure;
+        }
 
-      for (const [postfixPath, postfixValue] of Object.entries(
-        esp.equivalentPostfixes,
-      )) {
-        let relevantPostfix = postfixPath;
-        if (equivalentRoot.postfix) {
-          // Check if postfixPath starts with equivalentRoot.postfix at a path boundary.
-          // Must ensure exact path part match - "entityCode" should NOT match "entity" prefix.
-          // Valid: "entity.foo" starts with "entity" (boundary at '.')
-          // Valid: "entity[0]" starts with "entity" (boundary at '[')
-          // Invalid: "entityCode" starts with "entity" (no boundary, different property)
-          if (!postfixPath.startsWith(equivalentRoot.postfix)) {
-            continue;
-          }
-          // Additional check: ensure the match is at a path boundary
-          const nextChar = postfixPath[equivalentRoot.postfix.length];
-          if (nextChar !== undefined && nextChar !== '.' && nextChar !== '[') {
-            // The postfixPath continues with more characters that aren't a path separator.
-            // This means "entity" matched "entityCode" which is wrong - they're different properties.
-            continue;
-          }
+        if (!merged) continue;
 
-          const postFixPathParts =
-            splitOutsideParenthesesAndArrays(postfixPath);
-          const equivalentRootPostFixParts = splitOutsideParenthesesAndArrays(
-            equivalentRoot.postfix,
-          );
-          relevantPostfix = joinParenthesesAndArrays(
-            postFixPathParts.slice(equivalentRootPostFixParts.length),
-          );
-        }
+        const schema = equivalentRoot.schemaRootPath.startsWith('signature[')
+          ? merged.signatureSchema
+          : merged.returnValueSchema;
 
-        const newSchemaPath = joinParenthesesAndArrays([
-          equivalentRoot.schemaRootPath,
-          relevantPostfix,
-        ]);
+        // Skip if this schema has already grown past the cap
+        if (Object.keys(schema).length > SCHEMA_KEY_CAP) continue;
 
-        // Skip paths that would go through a primitive type
-        // e.g., if schema has 'entities[].scenarioCount': 'number', skip 'entities[].scenarioCount.sha'
-        if (wouldGoThroughPrimitive(newSchemaPath, schema)) {
-          continue;
-        }
+        for (const [postfixPath, postfixValue] of Object.entries(
+          esp.equivalentPostfixes,
+        )) {
+          checkDeadline();
+          let relevantPostfix = postfixPath;
+          if (equivalentRoot.postfix) {
+            // Check if postfixPath starts with equivalentRoot.postfix at a path boundary.
+            // Must ensure exact path part match - "entityCode" should NOT match "entity" prefix.
+            // Valid: "entity.foo" starts with "entity" (boundary at '.')
+            // Valid: "entity[0]" starts with "entity" (boundary at '[')
+            // Invalid: "entityCode" starts with "entity" (no boundary, different property)
+            if (!postfixPath.startsWith(equivalentRoot.postfix)) {
+              continue;
+            }
+            // Additional check: ensure the match is at a path boundary
+            const nextChar = postfixPath[equivalentRoot.postfix.length];
+            if (
+              nextChar !== undefined &&
+              nextChar !== '.' &&
+              nextChar !== '['
+            ) {
+              // The postfixPath continues with more characters that aren't a path separator.
+              // This means "entity" matched "entityCode" which is wrong - they're different properties.
+              continue;
+            }
 
-        // Skip setting primitive type when there are child postfixes that indicate structure.
-        // This prevents downgrading an object/array element to a primitive type.
-        // Uses pre-computed postfixesWithChildren Set for O(1) lookup instead of O(n) iteration.
-        const hasChildPostfixes =
-          (relevantPostfix === '' || relevantPostfix.endsWith('[]')) &&
-          postfixesWithChildren.has(postfixPath);
-        if (PRIMITIVE_TYPES.has(postfixValue) && hasChildPostfixes) {
-          continue;
-        }
+            const postFixPathParts =
+              postfixPartsCache.get(postfixPath) ??
+              splitOutsideParenthesesAndArrays(postfixPath);
+            // Cache equivalentRoot.postfix parts — same root reused across all postfixes
+            if (!postfixPartsCache.has(equivalentRoot.postfix)) {
+              postfixPartsCache.set(
+                equivalentRoot.postfix,
+                splitOutsideParenthesesAndArrays(equivalentRoot.postfix),
+              );
+            }
+            const equivalentRootPostFixParts = postfixPartsCache.get(
+              equivalentRoot.postfix,
+            )!;
+            relevantPostfix = joinParenthesesAndArrays(
+              postFixPathParts.slice(equivalentRootPostFixParts.length),
+            );
+          }
 
-        // Don't overwrite a more specific type with a less specific one
-        // This can happen when nested roots share entries with their parent roots
-        const existingType = schema[newSchemaPath];
-        if (existingType) {
-          // Don't overwrite a primitive type with 'object' or 'array'
-          // e.g., if schema has 'entities[].scenarioCount': 'number', don't overwrite with 'object'
-          if (
-            PRIMITIVE_TYPES.has(existingType) &&
-            (postfixValue === 'object' || postfixValue === 'array')
-          ) {
+          const newSchemaPath = joinParenthesesAndArrays([
+            equivalentRoot.schemaRootPath,
+            relevantPostfix,
+          ]);
+
+          // Skip paths that would go through a primitive type
+          // e.g., if schema has 'entities[].scenarioCount': 'number', skip 'entities[].scenarioCount.sha'
+          if (wouldGoThroughPrimitive(newSchemaPath, schema)) {
+            transformationTracer.operation(rootScopeName, {
+              operation: 'skipPrimitivePath',
+              stage: 'merged',
+              path: newSchemaPath,
+              context: {
+                reason: 'would go through primitive type',
+                postfixValue,
+              },
+            });
             continue;
           }
-          // Don't overwrite a complex/union type with a primitive
-          // e.g., if schema has 'scenarios[]': 'Scenario | null', don't overwrite with 'string'
-          if (
-            !PRIMITIVE_TYPES.has(existingType) &&
-            PRIMITIVE_TYPES.has(postfixValue)
-          ) {
+
+          // Skip setting primitive type when there are child postfixes that indicate structure.
+          // This prevents downgrading an object/array element to a primitive type.
+          // Uses pre-computed postfixesWithChildren Set for O(1) lookup instead of O(n) iteration.
+          const hasChildPostfixes =
+            (relevantPostfix === '' || relevantPostfix.endsWith('[]')) &&
+            postfixesWithChildren.has(postfixPath);
+          if (PRIMITIVE_TYPES.has(postfixValue) && hasChildPostfixes) {
             continue;
           }
+
+          // Don't overwrite a more specific type with a less specific one
+          // This can happen when nested roots share entries with their parent roots
+          const existingType = schema[newSchemaPath];
+          if (existingType) {
+            // Don't overwrite a primitive type with 'object' or 'array'
+            // e.g., if schema has 'entities[].scenarioCount': 'number', don't overwrite with 'object'
+            if (
+              PRIMITIVE_TYPES.has(existingType) &&
+              (postfixValue === 'object' || postfixValue === 'array')
+            ) {
+              transformationTracer.operation(rootScopeName, {
+                operation: 'skipTypeDowngrade',
+                stage: 'merged',
+                path: newSchemaPath,
+                context: {
+                  reason: 'would overwrite primitive with object/array',
+                  existingType,
+                  newType: postfixValue,
+                },
+              });
+              continue;
+            }
+            // Don't overwrite a complex/union type with a primitive
+            // e.g., if schema has 'scenarios[]': 'Scenario | null', don't overwrite with 'string'
+            if (
+              !PRIMITIVE_TYPES.has(existingType) &&
+              PRIMITIVE_TYPES.has(postfixValue)
+            ) {
+              transformationTracer.operation(rootScopeName, {
+                operation: 'skipTypeDowngrade',
+                stage: 'merged',
+                path: newSchemaPath,
+                context: {
+                  reason: 'would overwrite complex type with primitive',
+                  existingType,
+                  newType: postfixValue,
+                },
+              });
+              continue;
+            }
+          }
+
+          // Log the successful postfix merge
+          transformationTracer.operation(rootScopeName, {
+            operation: 'mergePostfix',
+            stage: 'merged',
+            path: newSchemaPath,
+            before: existingType,
+            after: postfixValue,
+            context: {
+              schemaRootPath: equivalentRoot.schemaRootPath,
+              postfix: relevantPostfix,
+              dependency: equivalentRoot.function?.name,
+            },
+          });
+          schema[newSchemaPath] = postfixValue;
         }
 
-        schema[newSchemaPath] = postfixValue;
+        schemasToClean.add(schema);
       }
+    }
+
+    const postfixElapsed = Date.now() - mergeStartTime;
 
-      cleanSchema(schema);
+    // Batch-clean all modified schemas once (instead of once per root per ESP entry)
+    for (const schema of schemasToClean) {
+      cleanSchema(schema, { stage: 'afterMergePostfix' });
     }
-  }
 
-  // Propagate equivalency-derived attributes to generic function call variants.
-  // When attributes are traced via equivalencies (e.g., fileComparisons from buildDataMap.signature[2]),
-  // they get written to non-generic paths (returnValue.data.x or funcName().functionCallReturnValue.data.x).
-  // If the ORIGINAL input schema has generic variants (funcName<T>().functionCallReturnValue.data),
-  // we need to copy the attributes to those paths too.
-  for (const filePath in mergedDataStructure.dependencySchemas) {
-    for (const depName in mergedDataStructure.dependencySchemas[filePath]) {
-      const depSchema =
-        mergedDataStructure.dependencySchemas[filePath][depName];
-      const returnValueSchema = depSchema.returnValueSchema;
-
-      // Look at the ORIGINAL input dependencySchemas for generic variants,
-      // since the merged schema may have lost them during equivalency processing
-      const originalSchema = dependencySchemas?.[filePath]?.[depName];
-      const schemaToSearchForGenericVariants =
-        originalSchema?.returnValueSchema || returnValueSchema;
-
-      // Find all unique generic variants of this function
-      // e.g., useFetcher<BranchEntityDiffResult>() from useFetcher<BranchEntityDiffResult>().functionCallReturnValue.data
-      const genericVariants = new Set<string>();
-      const genericRegex = new RegExp(
-        `^${depName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}<[^>]+>\\(\\)`,
-      );
+    const cleanElapsed = Date.now() - mergeStartTime;
+
+    // Propagate equivalency-derived attributes to generic function call variants.
+    // When attributes are traced via equivalencies (e.g., fileComparisons from buildDataMap.signature[2]),
+    // they get written to non-generic paths (returnValue.data.x or funcName().functionCallReturnValue.data.x).
+    // If the ORIGINAL input schema has generic variants (funcName<T>().functionCallReturnValue.data),
+    // we need to copy the attributes to those paths too.
+    for (const filePath in mergedDataStructure.dependencySchemas) {
+      for (const depName in mergedDataStructure.dependencySchemas[filePath]) {
+        const depSchema =
+          mergedDataStructure.dependencySchemas[filePath][depName];
+        const returnValueSchema = depSchema.returnValueSchema;
+
+        // Look at the ORIGINAL input dependencySchemas for generic variants,
+        // since the merged schema may have lost them during equivalency processing
+        const originalSchema = dependencySchemas?.[filePath]?.[depName];
+        const schemaToSearchForGenericVariants =
+          originalSchema?.returnValueSchema || returnValueSchema;
+
+        // Find all unique generic variants of this function
+        // e.g., useFetcher<BranchEntityDiffResult>() from useFetcher<BranchEntityDiffResult>().functionCallReturnValue.data
+        const genericVariants = new Set<string>();
+        const genericRegex = new RegExp(
+          `^${depName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}<[^>]+>\\(\\)`,
+        );
 
-      for (const path in schemaToSearchForGenericVariants) {
-        const match = path.match(genericRegex);
-        if (match) {
-          genericVariants.add(match[0]);
+        for (const path in schemaToSearchForGenericVariants) {
+          checkDeadline();
+          const match = path.match(genericRegex);
+          if (match) {
+            genericVariants.add(match[0]);
+          }
         }
-      }
 
-      if (genericVariants.size === 0) continue;
+        if (genericVariants.size === 0) continue;
 
-      // For each returnValue. path or non-generic function call path,
-      // create corresponding paths for each generic variant
-      const pathsToAdd: [string, string][] = [];
+        // For each returnValue. path or non-generic function call path,
+        // create corresponding paths for each generic variant
+        const pathsToAdd: [string, string][] = [];
 
-      for (const path in returnValueSchema) {
-        const value = returnValueSchema[path];
+        for (const path in returnValueSchema) {
+          checkDeadline();
+          const value = returnValueSchema[path];
 
-        // Handle returnValue. paths
-        if (path.startsWith('returnValue.')) {
-          const suffix = path.slice('returnValue.'.length);
-          for (const genericVariant of genericVariants) {
-            const genericPath = `${genericVariant}.functionCallReturnValue.${suffix}`;
-            if (!(genericPath in returnValueSchema)) {
-              pathsToAdd.push([genericPath, value]);
+          // Handle returnValue. paths
+          if (path.startsWith('returnValue.')) {
+            const suffix = path.slice('returnValue.'.length);
+            for (const genericVariant of genericVariants) {
+              const genericPath = `${genericVariant}.functionCallReturnValue.${suffix}`;
+              if (!(genericPath in returnValueSchema)) {
+                pathsToAdd.push([genericPath, value]);
+              }
             }
           }
-        }
-        // Handle non-generic function call paths like depName().functionCallReturnValue.x
-        else if (path.startsWith(`${depName}().functionCallReturnValue.`)) {
-          const suffix = path.slice(
-            `${depName}().functionCallReturnValue.`.length,
-          );
-          for (const genericVariant of genericVariants) {
-            const genericPath = `${genericVariant}.functionCallReturnValue.${suffix}`;
-            if (!(genericPath in returnValueSchema)) {
-              pathsToAdd.push([genericPath, value]);
+          // Handle non-generic function call paths like depName().functionCallReturnValue.x
+          else if (path.startsWith(`${depName}().functionCallReturnValue.`)) {
+            const suffix = path.slice(
+              `${depName}().functionCallReturnValue.`.length,
+            );
+            for (const genericVariant of genericVariants) {
+              const genericPath = `${genericVariant}.functionCallReturnValue.${suffix}`;
+              if (!(genericPath in returnValueSchema)) {
+                pathsToAdd.push([genericPath, value]);
+              }
             }
           }
         }
-      }
 
-      // Add the new generic variant paths
-      for (const [path, value] of pathsToAdd) {
-        returnValueSchema[path] = value;
+        // Add the new generic variant paths
+        for (const [path, value] of pathsToAdd) {
+          returnValueSchema[path] = value;
+        }
       }
     }
-  }
 
-  // For mocked dependencies: copy paths from dependencySchemas (usage info) and normalize
-  // returnValue. paths that were created by equivalency processing.
-  // This ensures all paths use the consistent functionName().functionCallReturnValue. format.
-  for (const dependency of importedExports) {
-    if (!dependency.isMocked) continue;
-
-    const srcSchema =
-      dependencySchemas?.[dependency.filePath]?.[dependency.name];
-    if (!srcSchema?.returnValueSchema) continue;
-
-    const depSchema = findOrCreateDependentSchemas({
-      filePath: dependency.filePath,
-      name: dependency.name,
-    });
-
-    // First, normalize any returnValue paths that were written by equivalency processing
-    // to the standard functionName().functionCallReturnValue format.
-    // This includes both returnValue. (dot) and returnValue[ (array) paths.
-    const pathsToNormalize: [string, string][] = [];
-    for (const path in depSchema.returnValueSchema) {
-      if (
-        path === 'returnValue' ||
-        path.startsWith('returnValue.') ||
-        path.startsWith('returnValue[')
-      ) {
-        pathsToNormalize.push([path, depSchema.returnValueSchema[path]]);
-      }
-    }
-    for (const [path, value] of pathsToNormalize) {
-      delete depSchema.returnValueSchema[path];
-      let normalizedPath: string;
-      if (path === 'returnValue') {
-        normalizedPath = `${dependency.name}().functionCallReturnValue`;
-      } else if (path.startsWith('returnValue.')) {
-        normalizedPath = path.replace(
-          /^returnValue\./,
-          `${dependency.name}().functionCallReturnValue.`,
-        );
-      } else {
-        // path.startsWith('returnValue[')
-        // e.g., returnValue[] -> getOptions().functionCallReturnValue[]
-        // e.g., returnValue[].label -> getOptions().functionCallReturnValue[].label
-        normalizedPath = path.replace(
-          /^returnValue/,
-          `${dependency.name}().functionCallReturnValue`,
-        );
+    // For mocked dependencies: copy paths from dependencySchemas (usage info) and normalize
+    // returnValue. paths that were created by equivalency processing.
+    // This ensures all paths use the consistent functionName().functionCallReturnValue. format.
+    for (const dependency of importedExports) {
+      if (!dependency.isMocked) continue;
+
+      const srcSchema =
+        dependencySchemas?.[dependency.filePath]?.[dependency.name];
+      if (!srcSchema?.returnValueSchema) continue;
+
+      const depSchema = findOrCreateDependentSchemas({
+        filePath: dependency.filePath,
+        name: dependency.name,
+      });
+
+      // First, normalize any returnValue paths that were written by equivalency processing
+      // to the standard functionName().functionCallReturnValue format.
+      // This includes both returnValue. (dot) and returnValue[ (array) paths.
+      const pathsToNormalize: [string, string][] = [];
+      for (const path in depSchema.returnValueSchema) {
+        checkDeadline();
+        if (
+          path === 'returnValue' ||
+          path.startsWith('returnValue.') ||
+          path.startsWith('returnValue[')
+        ) {
+          pathsToNormalize.push([path, depSchema.returnValueSchema[path]]);
+        }
       }
-      depSchema.returnValueSchema[normalizedPath] = value;
-    }
-
-    // Now copy paths from the source schema (dependencySchemas)
-    for (const path in srcSchema.returnValueSchema) {
-      const value = srcSchema.returnValueSchema[path];
-
-      // Normalize paths starting with 'returnValue' to use the standard format:
-      // 'returnValue.foo' -> 'dependencyName().functionCallReturnValue.foo'
-      // This ensures consistency across the codebase and allows constructMockCode
-      // and gatherDataForMocks to work correctly.
-      if (path === 'returnValue' || path.startsWith('returnValue.')) {
-        // Convert 'returnValue' -> 'name().functionCallReturnValue'
-        // Convert 'returnValue.foo' -> 'name().functionCallReturnValue.foo'
-        const normalizedPath =
-          path === 'returnValue'
-            ? `${dependency.name}().functionCallReturnValue`
-            : path.replace(
-                /^returnValue\./,
-                `${dependency.name}().functionCallReturnValue.`,
-              );
-
-        // Always write srcSchema values - they take precedence over equivalency-derived values
+      for (const [path, value] of pathsToNormalize) {
+        delete depSchema.returnValueSchema[path];
+        let normalizedPath: string;
+        if (path === 'returnValue') {
+          normalizedPath = `${dependency.name}().functionCallReturnValue`;
+        } else if (path.startsWith('returnValue.')) {
+          normalizedPath = path.replace(
+            /^returnValue\./,
+            `${dependency.name}().functionCallReturnValue.`,
+          );
+        } else {
+          // path.startsWith('returnValue[')
+          // e.g., returnValue[] -> getOptions().functionCallReturnValue[]
+          // e.g., returnValue[].label -> getOptions().functionCallReturnValue[].label
+          normalizedPath = path.replace(
+            /^returnValue/,
+            `${dependency.name}().functionCallReturnValue`,
+          );
+        }
+        transformationTracer.operation(rootScopeName, {
+          operation: 'normalizeReturnValuePath',
+          stage: 'merged',
+          path: normalizedPath,
+          before: path,
+          after: normalizedPath,
+          context: { dependency: dependency.name, value },
+        });
         depSchema.returnValueSchema[normalizedPath] = value;
-        continue;
       }
 
-      // Copy paths containing functionCallReturnValue (return value structures)
-      // These are needed for constructMockCode to build the proper mock data hierarchy
-      // Example: supabase.auth.getSession().functionCallReturnValue.data.session
-      if (path.includes('.functionCallReturnValue')) {
-        // Always write srcSchema values - they take precedence over equivalency-derived values
-        depSchema.returnValueSchema[path] = value;
-        continue;
-      }
+      // Now copy paths from the source schema (dependencySchemas)
+      for (const path in srcSchema.returnValueSchema) {
+        checkDeadline();
+        const value = srcSchema.returnValueSchema[path];
+
+        // Normalize paths starting with 'returnValue' to use the standard format:
+        // 'returnValue.foo' -> 'dependencyName().functionCallReturnValue.foo'
+        // This ensures consistency across the codebase and allows constructMockCode
+        // and gatherDataForMocks to work correctly.
+        if (path === 'returnValue' || path.startsWith('returnValue.')) {
+          // Convert 'returnValue' -> 'name().functionCallReturnValue'
+          // Convert 'returnValue.foo' -> 'name().functionCallReturnValue.foo'
+          const normalizedPath =
+            path === 'returnValue'
+              ? `${dependency.name}().functionCallReturnValue`
+              : path.replace(
+                  /^returnValue\./,
+                  `${dependency.name}().functionCallReturnValue.`,
+                );
 
-      // Copy function-typed paths that end with () (are function calls)
-      // These include:
-      // - Function stubs without functionCallReturnValue (like onAuthStateChange)
-      // - Function markers with async-function type (like getSession(): async-function)
-      //   which are needed for constructMockCode to know to generate async functions
-      // Skip paths starting with 'returnValue' - they were already handled above
-      if (
-        ['function', 'async-function'].includes(value) &&
-        path.endsWith(')') &&
-        !path.startsWith('returnValue')
-      ) {
-        if (!(path in depSchema.returnValueSchema)) {
+          // Always write srcSchema values - they take precedence over equivalency-derived values
+          depSchema.returnValueSchema[normalizedPath] = value;
+          continue;
+        }
+
+        // Copy paths containing functionCallReturnValue (return value structures)
+        // These are needed for constructMockCode to build the proper mock data hierarchy
+        // Example: supabase.auth.getSession().functionCallReturnValue.data.session
+        if (path.includes('.functionCallReturnValue')) {
+          // Always write srcSchema values - they take precedence over equivalency-derived values
           depSchema.returnValueSchema[path] = value;
+          continue;
         }
-      }
 
-      // Copy object-typed paths for chained API access patterns (like trpc.customer.getCustomersByOrg)
-      // These intermediate paths are needed for constructMockCode to build the nested mock structure.
-      // Example: for trpc.customer.getCustomersByOrg.useQuery().functionCallReturnValue.data,
-      // we need 'trpc', 'trpc.customer', 'trpc.customer.getCustomersByOrg' all typed as 'object'.
-      // Skip paths starting with 'returnValue' - they were already handled above
-      //
-      // EXCEPTION: For function-style dependencies like getSupabase(), skip intermediate object
-      // paths like 'getSupabase().auth' that are just property access after a function call.
-      // These aren't needed because constructMockCode can infer the structure from the actual
-      // function call paths like 'getSupabase().auth.getUser()'. We only need object paths
-      // for object-style dependencies like 'supabase.auth' where the dependency itself is an object.
-      if (value === 'object' && !path.startsWith('returnValue')) {
-        // Check if this is a function-style dependency (path starts with name() or name<T>())
-        const isFunctionStyleDependency =
-          path.startsWith(`${dependency.name}()`) ||
-          path.match(new RegExp(`^${dependency.name}<[^>]+>\\(\\)`));
-
-        // For function-style dependencies, skip intermediate object paths
-        // Only keep object paths that are within functionCallReturnValue
+        // Copy function-typed paths that end with () (are function calls)
+        // These include:
+        // - Function stubs without functionCallReturnValue (like onAuthStateChange)
+        // - Function markers with async-function type (like getSession(): async-function)
+        //   which are needed for constructMockCode to know to generate async functions
+        // Skip paths starting with 'returnValue' - they were already handled above
         if (
-          isFunctionStyleDependency &&
-          !path.includes('.functionCallReturnValue')
+          ['function', 'async-function'].includes(value) &&
+          path.endsWith(')') &&
+          !path.startsWith('returnValue')
         ) {
-          continue;
+          if (!(path in depSchema.returnValueSchema)) {
+            depSchema.returnValueSchema[path] = value;
+          }
         }
 
-        if (!(path in depSchema.returnValueSchema)) {
-          depSchema.returnValueSchema[path] = value;
+        // Copy object-typed paths for chained API access patterns (like trpc.customer.getCustomersByOrg)
+        // These intermediate paths are needed for constructMockCode to build the nested mock structure.
+        // Example: for trpc.customer.getCustomersByOrg.useQuery().functionCallReturnValue.data,
+        // we need 'trpc', 'trpc.customer', 'trpc.customer.getCustomersByOrg' all typed as 'object'.
+        // Skip paths starting with 'returnValue' - they were already handled above
+        //
+        // EXCEPTION: For function-style dependencies like getSupabase(), skip intermediate object
+        // paths like 'getSupabase().auth' that are just property access after a function call.
+        // These aren't needed because constructMockCode can infer the structure from the actual
+        // function call paths like 'getSupabase().auth.getUser()'. We only need object paths
+        // for object-style dependencies like 'supabase.auth' where the dependency itself is an object.
+        if (value === 'object' && !path.startsWith('returnValue')) {
+          // Check if this is a function-style dependency (path starts with name() or name<T>())
+          const isFunctionStyleDependency =
+            path.startsWith(`${dependency.name}()`) ||
+            path.match(new RegExp(`^${dependency.name}<[^>]+>\\(\\)`));
+
+          // For function-style dependencies, skip intermediate object paths
+          // Only keep object paths that are within functionCallReturnValue
+          if (
+            isFunctionStyleDependency &&
+            !path.includes('.functionCallReturnValue')
+          ) {
+            continue;
+          }
+
+          if (!(path in depSchema.returnValueSchema)) {
+            depSchema.returnValueSchema[path] = value;
+          }
         }
       }
-    }
 
-    cleanSchema(depSchema.returnValueSchema);
+      cleanSchema(depSchema.returnValueSchema, {
+        stage: 'afterMockedDependencyMerge',
+        dependency: dependency.name,
+      });
 
-    // Pull signature requirements from downstream functions into the mocked return value.
-    // When a mocked function's return flows into another function's signature (via usageEquivalencies),
-    // we need to include that function's signature requirements in the mock.
-    //
-    // Example: fromE5() returns a currency object that flows to calculateTotalPrice(price, quantity).
-    // calculateTotalPrice's signatureSchema shows signature[0].multiply() is required.
-    // We need to add multiply() to fromE5's mock return value.
-    const usageEquivalencies = srcSchema.usageEquivalencies ?? {};
-    for (const [returnPath, equivalencies] of Object.entries(
-      usageEquivalencies,
-    )) {
-      // Only process return value paths (functionCallReturnValue)
-      if (!returnPath.includes('.functionCallReturnValue')) continue;
-
-      for (const equiv of equivalencies) {
-        // Check if this equivalency points to a signature path
-        const signatureMatch = equiv.schemaPath.match(/\.signature\[(\d+)\]$/);
-        if (!signatureMatch) continue;
-
-        const targetFunctionName = cleanFunctionName(equiv.scopeNodeName);
-        const signatureIndex = signatureMatch[1];
-
-        // Look up the target function's analysis to get its signature requirements
-        // First try dependentAnalyses, then dependencySchemas
-        let targetSignatureSchema: Record<string, string> | undefined;
-
-        // Check dependentAnalyses first (has the full merged analysis)
-        for (const depFilePath in dependentAnalyses) {
-          const analysis = dependentAnalyses[depFilePath]?.[targetFunctionName];
-          if (analysis?.metadata?.mergedDataStructure?.signatureSchema) {
-            targetSignatureSchema =
-              analysis.metadata.mergedDataStructure.signatureSchema;
-            break;
-          }
-        }
+      // Pull signature requirements from downstream functions into the mocked return value.
+      // When a mocked function's return flows into another function's signature (via usageEquivalencies),
+      // we need to include that function's signature requirements in the mock.
+      //
+      // Example: fromE5() returns a currency object that flows to calculateTotalPrice(price, quantity).
+      // calculateTotalPrice's signatureSchema shows signature[0].multiply() is required.
+      // We need to add multiply() to fromE5's mock return value.
+      const usageEquivalencies = srcSchema.usageEquivalencies ?? {};
+      for (const [returnPath, equivalencies] of Object.entries(
+        usageEquivalencies,
+      )) {
+        // Only process return value paths (functionCallReturnValue)
+        if (!returnPath.includes('.functionCallReturnValue')) continue;
 
-        // Fallback to dependencySchemas if not found
-        if (!targetSignatureSchema) {
-          for (const depFilePath in dependencySchemas) {
-            const schema = dependencySchemas[depFilePath]?.[targetFunctionName];
-            if (schema?.signatureSchema) {
-              targetSignatureSchema = schema.signatureSchema;
+        for (const equiv of equivalencies) {
+          // Check if this equivalency points to a signature path
+          const signatureMatch = equiv.schemaPath.match(
+            /\.signature\[(\d+)\]$/,
+          );
+          if (!signatureMatch) continue;
+
+          const targetFunctionName = cleanFunctionName(equiv.scopeNodeName);
+          const signatureIndex = signatureMatch[1];
+
+          // Look up the target function's analysis to get its signature requirements
+          // First try dependentAnalyses, then dependencySchemas
+          let targetSignatureSchema: Record<string, string> | undefined;
+
+          // Check dependentAnalyses first (has the full merged analysis)
+          for (const depFilePath in dependentAnalyses) {
+            const analysis =
+              dependentAnalyses[depFilePath]?.[targetFunctionName];
+            if (analysis?.metadata?.mergedDataStructure?.signatureSchema) {
+              targetSignatureSchema =
+                analysis.metadata.mergedDataStructure.signatureSchema;
               break;
             }
           }
-        }
 
-        if (!targetSignatureSchema) continue;
+          // Fallback to dependencySchemas if not found
+          if (!targetSignatureSchema) {
+            for (const depFilePath in dependencySchemas) {
+              const schema =
+                dependencySchemas[depFilePath]?.[targetFunctionName];
+              if (schema?.signatureSchema) {
+                targetSignatureSchema = schema.signatureSchema;
+                break;
+              }
+            }
+          }
 
-        // Find all paths in the target's signatureSchema that extend from signature[N]
-        // e.g., signature[0].multiply(quantity) -> .multiply(quantity)
-        const signaturePrefix = `signature[${signatureIndex}]`;
-        for (const [sigPath, sigType] of Object.entries(
-          targetSignatureSchema,
-        )) {
-          if (!sigPath.startsWith(signaturePrefix)) continue;
+          if (!targetSignatureSchema) continue;
+
+          // Find all paths in the target's signatureSchema that extend from signature[N]
+          // e.g., signature[0].multiply(quantity) -> .multiply(quantity)
+          const signaturePrefix = `signature[${signatureIndex}]`;
+          for (const [sigPath, sigType] of Object.entries(
+            targetSignatureSchema,
+          )) {
+            if (!sigPath.startsWith(signaturePrefix)) continue;
 
-          // Skip the base signature[N] path itself - we only want the method/property extensions
-          if (sigPath === signaturePrefix) continue;
+            // Skip the base signature[N] path itself - we only want the method/property extensions
+            if (sigPath === signaturePrefix) continue;
 
-          // Extract the suffix after signature[N] (e.g., ".multiply(quantity)")
-          const suffix = sigPath.slice(signaturePrefix.length);
+            // Extract the suffix after signature[N] (e.g., ".multiply(quantity)")
+            const suffix = sigPath.slice(signaturePrefix.length);
 
-          // Build the path for the mocked return value
-          // e.g., fromE5(priceE5).functionCallReturnValue.multiply(quantity)
-          const returnValuePath = returnPath + suffix;
+            // Build the path for the mocked return value
+            // e.g., fromE5(priceE5).functionCallReturnValue.multiply(quantity)
+            const returnValuePath = returnPath + suffix;
 
-          // Add to the mocked dependency's return value schema if not already present
-          if (!(returnValuePath in depSchema.returnValueSchema)) {
-            depSchema.returnValueSchema[returnValuePath] = sigType;
+            // Add to the mocked dependency's return value schema if not already present
+            if (!(returnValuePath in depSchema.returnValueSchema)) {
+              depSchema.returnValueSchema[returnValuePath] = sigType;
+            }
           }
         }
       }
+
+      cleanSchema(depSchema.returnValueSchema, {
+        stage: 'afterSignatureRequirementsMerge',
+        dependency: dependency.name,
+      });
     }
 
-    cleanSchema(depSchema.returnValueSchema);
-  }
+    // Process the input dependencySchemas FIRST (before child dependentAnalyses).
+    // This ensures the parent entity's direct usage of dependencies takes precedence.
+    // When both parent and child use the same dependency (e.g., useLoaderData),
+    // the parent's schema paths are preserved, and child's paths are merged in later.
+    //
+    // Some dependencies (like .d.ts type declaration files) may not have:
+    // - Equivalencies with the root scope
+    // - A dependent analysis (they're just type declarations)
+    // - Be marked as mocked
+    // Without this, their schemas would be lost entirely.
+    for (const filePath in dependencySchemas) {
+      for (const name in dependencySchemas[filePath]) {
+        const srcSchema = dependencySchemas[filePath][name];
+        if (!srcSchema) continue;
+
+        // Skip mocked dependencies - they were already processed above with path normalization
+        if (mockedDependencies.has(`${filePath}::${name}`)) {
+          continue;
+        }
 
-  // Process the input dependencySchemas FIRST (before child dependentAnalyses).
-  // This ensures the parent entity's direct usage of dependencies takes precedence.
-  // When both parent and child use the same dependency (e.g., useLoaderData),
-  // the parent's schema paths are preserved, and child's paths are merged in later.
-  //
-  // Some dependencies (like .d.ts type declaration files) may not have:
-  // - Equivalencies with the root scope
-  // - A dependent analysis (they're just type declarations)
-  // - Be marked as mocked
-  // Without this, their schemas would be lost entirely.
-  for (const filePath in dependencySchemas) {
-    for (const name in dependencySchemas[filePath]) {
-      const srcSchema = dependencySchemas[filePath][name];
-      if (!srcSchema) continue;
-
-      // Skip mocked dependencies - they were already processed above with path normalization
-      if (mockedDependencies.has(`${filePath}::${name}`)) {
-        continue;
-      }
+        // Check if this dependency was already processed by equivalencies
+        const existingSchema =
+          mergedDataStructure.dependencySchemas[filePath]?.[name];
 
-      // Check if this dependency was already processed by equivalencies
-      const existingSchema =
-        mergedDataStructure.dependencySchemas[filePath]?.[name];
+        // Only add if no existing schema (equivalencies didn't process it)
+        if (!existingSchema) {
+          const depSchema = findOrCreateDependentSchemas({ filePath, name });
+          for (const path in srcSchema.returnValueSchema) {
+            checkDeadline();
+            depSchema.returnValueSchema[path] =
+              srcSchema.returnValueSchema[path];
+          }
+          for (const path in srcSchema.signatureSchema) {
+            checkDeadline();
+            depSchema.signatureSchema[path] = srcSchema.signatureSchema[path];
+          }
 
-      // Only add if no existing schema (equivalencies didn't process it)
-      if (!existingSchema) {
-        const depSchema = findOrCreateDependentSchemas({ filePath, name });
-        for (const path in srcSchema.returnValueSchema) {
-          depSchema.returnValueSchema[path] = srcSchema.returnValueSchema[path];
-        }
-        for (const path in srcSchema.signatureSchema) {
-          depSchema.signatureSchema[path] = srcSchema.signatureSchema[path];
+          // Clean known object functions (like String.prototype.replace, Array.prototype.map)
+          // from the copied schema. Without this, method call paths on primitives like
+          // "projectSlug.replace(...)" would cause convertDotNotation to create nested
+          // object structures instead of preserving the primitive type.
+          cleanSchema(depSchema.returnValueSchema, {
+            stage: 'afterDependencySchemaCopy',
+            filePath,
+            dependency: name,
+          });
         }
 
-        // Clean known object functions (like String.prototype.replace, Array.prototype.map)
-        // from the copied schema. Without this, method call paths on primitives like
-        // "projectSlug.replace(...)" would cause convertDotNotation to create nested
-        // object structures instead of preserving the primitive type.
-        cleanSchema(depSchema.returnValueSchema);
-      }
-
-      // TYPE REFINEMENT: Check if dependentAnalyses has a more specific type for this dependency.
-      // When a parent passes `entity.filePath` (string | undefined) to a child component
-      // that requires `filePath: string`, we should use the child's more specific type.
-      // This prevents mock data from having undefined values for required props.
-      //
-      // This runs REGARDLESS of whether equivalencies already processed the schema,
-      // because equivalencies copy the parent's type (string | undefined), not the child's
-      // required type (string).
-      const depSchema = findOrCreateDependentSchemas({ filePath, name });
-      const childAnalysis = dependentAnalyses[filePath]?.[name];
-      const childSignatureSchema =
-        childAnalysis?.metadata?.mergedDataStructure?.signatureSchema;
-
-      if (childSignatureSchema) {
-        for (const path in depSchema.signatureSchema) {
-          const parentType = depSchema.signatureSchema[path];
-          const childType = childSignatureSchema[path];
-
-          if (parentType && childType) {
-            // Check if parent has optional type and child has required type
-            const parentIsOptional =
-              parentType.includes('| undefined') ||
-              parentType.includes('| null');
-            const childIsOptional =
-              childType.includes('| undefined') || childType.includes('| null');
-
-            // If child requires a more specific type (not optional), use it
-            if (parentIsOptional && !childIsOptional) {
-              depSchema.signatureSchema[path] = childType;
+        // TYPE REFINEMENT: Check if dependentAnalyses has a more specific type for this dependency.
+        // When a parent passes `entity.filePath` (string | undefined) to a child component
+        // that requires `filePath: string`, we should use the child's more specific type.
+        // This prevents mock data from having undefined values for required props.
+        //
+        // This runs REGARDLESS of whether equivalencies already processed the schema,
+        // because equivalencies copy the parent's type (string | undefined), not the child's
+        // required type (string).
+        const depSchema = findOrCreateDependentSchemas({ filePath, name });
+        const childAnalysis = dependentAnalyses[filePath]?.[name];
+        const childSignatureSchema =
+          childAnalysis?.metadata?.mergedDataStructure?.signatureSchema;
+
+        if (childSignatureSchema) {
+          for (const path in depSchema.signatureSchema) {
+            checkDeadline();
+            const parentType = depSchema.signatureSchema[path];
+            const childType = childSignatureSchema[path];
+
+            if (parentType && childType) {
+              // Check if parent has optional type and child has required type
+              const parentIsOptional =
+                parentType.includes('| undefined') ||
+                parentType.includes('| null');
+              const childIsOptional =
+                childType.includes('| undefined') ||
+                childType.includes('| null');
+
+              // If child requires a more specific type (not optional), use it
+              if (parentIsOptional && !childIsOptional) {
+                depSchema.signatureSchema[path] = childType;
+              }
             }
           }
         }
-      }
 
-      // For functions with multiple different type parameters, also create separate entries
-      // for each type-parameterized variant. This allows gatherDataForMocks to look up
-      // the specific schema for each call signature.
-      // This runs regardless of whether the base entry already existed, since we need
-      // the separate variant entries for proper schema lookup.
-      const baseName = cleanFunctionName(name);
-      if (functionsWithMultipleTypeParams.has(baseName)) {
-        // Find all unique type-parameterized call signatures in the schema
-        const typeParamVariants = new Set<string>();
-        for (const path of Object.keys(srcSchema.returnValueSchema)) {
-          const parts = splitOutsideParenthesesAndArrays(path);
-          if (
-            parts.length > 0 &&
-            parts[0].includes('<') &&
-            parts[0].endsWith(')')
-          ) {
-            typeParamVariants.add(parts[0]);
+        // For functions with multiple different type parameters, also create separate entries
+        // for each type-parameterized variant. This allows gatherDataForMocks to look up
+        // the specific schema for each call signature.
+        // This runs regardless of whether the base entry already existed, since we need
+        // the separate variant entries for proper schema lookup.
+        const baseName = cleanFunctionName(name);
+        if (functionsWithMultipleTypeParams.has(baseName)) {
+          // Find all unique type-parameterized call signatures in the schema
+          const typeParamVariants = new Set<string>();
+          for (const path of Object.keys(srcSchema.returnValueSchema)) {
+            const parts = splitOutsideParenthesesAndArrays(path);
+            if (
+              parts.length > 0 &&
+              parts[0].includes('<') &&
+              parts[0].endsWith(')')
+            ) {
+              typeParamVariants.add(parts[0]);
+            }
           }
-        }
 
-        // Create a separate entry for each type-parameterized variant
-        for (const variant of typeParamVariants) {
-          const variantSchema = findOrCreateDependentSchemas({
-            filePath,
-            name: variant,
-          });
+          // Create a separate entry for each type-parameterized variant
+          for (const variant of typeParamVariants) {
+            const variantSchema = findOrCreateDependentSchemas({
+              filePath,
+              name: variant,
+            });
 
-          // Copy only paths that belong to this variant
-          for (const path in srcSchema.returnValueSchema) {
-            if (path.startsWith(variant)) {
-              variantSchema.returnValueSchema[path] =
-                srcSchema.returnValueSchema[path];
+            // Copy only paths that belong to this variant
+            for (const path in srcSchema.returnValueSchema) {
+              checkDeadline();
+              if (path.startsWith(variant)) {
+                variantSchema.returnValueSchema[path] =
+                  srcSchema.returnValueSchema[path];
+              }
             }
+            cleanSchema(variantSchema.returnValueSchema, {
+              stage: 'afterTypeVariantCopy',
+              filePath,
+              dependency: name,
+              variant,
+            });
           }
-          cleanSchema(variantSchema.returnValueSchema);
         }
       }
     }
-  }
-
-  // Ensure ALL dependencies from dependentAnalyses are included in dependencySchemas,
-  // even if they have no equivalencies with the root scope.
-  // This preserves nested functionCallReturnValue paths that would otherwise be lost.
-  // EXCEPT: Skip mocked dependencies - we don't want their internal implementation details.
-  for (const filePath in dependentAnalyses) {
-    for (const name in dependentAnalyses[filePath]) {
-      const dependentMergedDataStructure =
-        dependentAnalyses[filePath][name].metadata?.mergedDataStructure;
-
-      if (!dependentMergedDataStructure) continue;
-
-      const isMocked = mockedDependencies.has(`${filePath}::${name}`);
-
-      // For mocked dependencies: ONLY copy nested dependencySchemas (skip internal implementation)
-      // For non-mocked dependencies: copy everything (signature, returnValue, and nested dependencySchemas)
-      if (!isMocked) {
-        // Create the dependency schema entry if it doesn't exist
-        const depSchema = findOrCreateDependentSchemas({ filePath, name });
 
-        // Copy over all paths from the dependent's returnValueSchema
-        // Only add paths that don't already exist (don't overwrite values set by equivalencies)
-        for (const path in dependentMergedDataStructure.returnValueSchema) {
-          const translatedPath = translatePath(path, name);
-          if (!(translatedPath in depSchema.returnValueSchema)) {
-            depSchema.returnValueSchema[translatedPath] =
-              dependentMergedDataStructure.returnValueSchema[path];
+    // Ensure ALL dependencies from dependentAnalyses are included in dependencySchemas,
+    // even if they have no equivalencies with the root scope.
+    // This preserves nested functionCallReturnValue paths that would otherwise be lost.
+    // EXCEPT: Skip mocked dependencies - we don't want their internal implementation details.
+    for (const filePath in dependentAnalyses) {
+      for (const name in dependentAnalyses[filePath]) {
+        checkDeadline();
+        const dependentMergedDataStructure =
+          dependentAnalyses[filePath][name].metadata?.mergedDataStructure;
+
+        if (!dependentMergedDataStructure) continue;
+
+        const isMocked = mockedDependencies.has(`${filePath}::${name}`);
+
+        // For mocked dependencies: ONLY copy nested dependencySchemas (skip internal implementation)
+        // For non-mocked dependencies: copy everything (signature, returnValue, and nested dependencySchemas)
+        if (!isMocked) {
+          // Create the dependency schema entry if it doesn't exist
+          const depSchema = findOrCreateDependentSchemas({ filePath, name });
+
+          // Copy over paths from the dependent's returnValueSchema.
+          // Only add paths that don't already exist (don't overwrite values set by equivalencies).
+          // Skip if either source or target exceeds the cap — copying 2,531 paths from
+          // ArticleTable with translatePath on each takes ~1.5s for one entity.
+          const srcRetSize = Object.keys(
+            dependentMergedDataStructure.returnValueSchema || {},
+          ).length;
+          if (
+            srcRetSize > SCHEMA_KEY_CAP ||
+            Object.keys(depSchema.returnValueSchema).length > SCHEMA_KEY_CAP
+          )
+            continue;
+          for (const path in dependentMergedDataStructure.returnValueSchema) {
+            // Fast path: only call translatePath when the path starts with the
+            // dependency name (e.g., "ArticleTable().functionCallReturnValue.x").
+            // Most paths start with "returnValue" or "signature" and don't need translation.
+            const translatedPath = path.startsWith(name)
+              ? translatePath(path, name)
+              : path;
+            if (!(translatedPath in depSchema.returnValueSchema)) {
+              depSchema.returnValueSchema[translatedPath] =
+                dependentMergedDataStructure.returnValueSchema[path];
+            }
           }
-        }
 
-        // Copy over signature schema as well
-        for (const path in dependentMergedDataStructure.signatureSchema) {
-          const translatedPath = translatePath(path, name);
-          if (!(translatedPath in depSchema.signatureSchema)) {
-            depSchema.signatureSchema[translatedPath] =
-              dependentMergedDataStructure.signatureSchema[path];
+          // Copy over signature schema as well
+          for (const path in dependentMergedDataStructure.signatureSchema) {
+            const translatedPath = path.startsWith(name)
+              ? translatePath(path, name)
+              : path;
+            if (!(translatedPath in depSchema.signatureSchema)) {
+              depSchema.signatureSchema[translatedPath] =
+                dependentMergedDataStructure.signatureSchema[path];
+            }
           }
         }
-      }
 
-      // Copy nested dependencySchemas for ALL entities (including mocked ones)
-      // This represents what dependencies THIS entity uses, not its internal implementation
-      if (dependentMergedDataStructure.dependencySchemas) {
-        for (const depFilePath in dependentMergedDataStructure.dependencySchemas) {
-          for (const depName in dependentMergedDataStructure.dependencySchemas[
-            depFilePath
-          ]) {
-            const nestedDepSchema =
-              dependentMergedDataStructure.dependencySchemas[depFilePath][
-                depName
-              ];
-            const targetDepSchema = findOrCreateDependentSchemas({
-              filePath: depFilePath,
-              name: depName,
-            });
-
-            // Merge in the nested dependency schemas
-            for (const path in nestedDepSchema.returnValueSchema) {
-              if (!(path in targetDepSchema.returnValueSchema)) {
-                const value = nestedDepSchema.returnValueSchema[path];
-                targetDepSchema.returnValueSchema[path] = value;
+        // Copy nested dependencySchemas for ALL entities (including mocked ones)
+        // This represents what dependencies THIS entity uses, not its internal implementation
+        if (dependentMergedDataStructure.dependencySchemas) {
+          for (const depFilePath in dependentMergedDataStructure.dependencySchemas) {
+            for (const depName in dependentMergedDataStructure
+              .dependencySchemas[depFilePath]) {
+              const nestedDepSchema =
+                dependentMergedDataStructure.dependencySchemas[depFilePath][
+                  depName
+                ];
+              const targetDepSchema = findOrCreateDependentSchemas({
+                filePath: depFilePath,
+                name: depName,
+              });
+
+              // Merge in the nested dependency schemas
+              for (const path in nestedDepSchema.returnValueSchema) {
+                checkDeadline();
+                if (!(path in targetDepSchema.returnValueSchema)) {
+                  const value = nestedDepSchema.returnValueSchema[path];
+                  targetDepSchema.returnValueSchema[path] = value;
+                }
               }
-            }
 
-            for (const path in nestedDepSchema.signatureSchema) {
-              if (!(path in targetDepSchema.signatureSchema)) {
-                targetDepSchema.signatureSchema[path] =
-                  nestedDepSchema.signatureSchema[path];
+              for (const path in nestedDepSchema.signatureSchema) {
+                checkDeadline();
+                if (!(path in targetDepSchema.signatureSchema)) {
+                  targetDepSchema.signatureSchema[path] =
+                    nestedDepSchema.signatureSchema[path];
+                }
               }
             }
           }
         }
       }
     }
-  }
 
-  return mergedDataStructure;
+    const totalElapsed = Date.now() - mergeStartTime;
+    const retKeys = Object.keys(mergedDataStructure.returnValueSchema).length;
+
+    // Only log phase breakdown for slow merges (>2s)
+    if (totalElapsed > 2000) {
+      console.log(
+        `CodeYam Log Level 2: ${rootScopeName} merge phases: gather=${gatherElapsed}ms mergeESP=${mergeEspElapsed - gatherElapsed}ms postfix=${postfixElapsed - mergeEspElapsed}ms clean=${cleanElapsed - postfixElapsed}ms depCopy=${totalElapsed - cleanElapsed}ms total=${totalElapsed}ms ret=${retKeys}`,
+      );
+    }
+
+    return mergedDataStructure;
+  } catch (error) {
+    if (error instanceof DataStructureTimeoutError) {
+      // Return partial results instead of propagating the timeout.
+      // By this point, mergedDataStructure has valid data from completed phases
+      // (gather + mergeESP complete in <1s, postfix/clean/depCopy may be partial).
+      const retKeys = Object.keys(mergedDataStructure.returnValueSchema).length;
+      console.log(
+        `CodeYam Log Level 1: ${rootScopeName} merge timed out — returning partial results (${retKeys} ret keys, ${Math.round((Date.now() - mergeStartTime) / 1000)}s)`,
+      );
+      (mergedDataStructure as any).timedOut = true;
+      return mergedDataStructure;
+    }
+    throw error;
+  }
 }