@codeyam/codeyam-cli 0.1.0-staging.483fdc2 → 0.1.0-staging.50df560

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 };
@@ -51,6 +52,7 @@ 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 +60,26 @@ 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 +117,21 @@ 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');
@@ -202,6 +229,23 @@ export default function mergeInDependentDataStructure({
     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);
+    }
+  };
+
   // 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<
@@ -253,8 +297,17 @@ export default function mergeInDependentDataStructure({
     return mergedDataStructure.dependencySchemas[filePath][name];
   };
 
-  const cleanSchema = (schema: { [key: string]: string }) => {
-    cleanKnownObjectFunctionsFromMapping(schema);
+  const cleanSchema = (
+    schema: { [key: string]: string },
+    context?: Record<string, any>,
+  ) => {
+    transformationTracer.traceSchemaTransform(
+      rootScopeName,
+      'cleanKnownObjectFunctionsFromMapping',
+      schema,
+      cleanKnownObjectFunctionsFromMapping,
+      context,
+    );
   };
 
   const translatePath = (path: string, dependencyName: string) => {
@@ -307,6 +360,54 @@ export default function mergeInDependentDataStructure({
   ) => {
     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) {
+        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 }[],
     ) => {
@@ -327,25 +428,102 @@ export default function mergeInDependentDataStructure({
       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) {
-        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)),
-            ),
-          );
+        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) {
+        // 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);
+          }
+
+          // 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;
+          });
+        }
+
         equivalentSchemaPathsEntry = {
-          equivalentRoots,
+          equivalentRoots: filteredRoots,
           equivalentPostfixes: {},
         };
         equivalentSchemaPaths.push(equivalentSchemaPathsEntry);
@@ -363,6 +541,9 @@ export default function mergeInDependentDataStructure({
           return true;
         });
 
+      // Keep the espIndex in sync after adding/deduplicating roots
+      updateEspIndex(equivalentSchemaPathsEntry);
+
       return equivalentSchemaPathsEntry;
     };
 
@@ -431,6 +612,8 @@ export default function mergeInDependentDataStructure({
         );
 
         const derivedBasePaths: { path: string; functionName?: string }[] = [];
+        const allPathSet = new Set(allPaths.map((p) => p.path));
+        const derivedBasePathSet = new Set<string>();
 
         // For each child path, find its equivalent parent path and derive bases
         for (const childPathInfo of childPaths) {
@@ -507,26 +690,28 @@ export default function mergeInDependentDataStructure({
                   !childHasArrayIterator &&
                   !childBaseIsGenericSignature
                 ) {
-                  // Add child base if not already present
-                  const childBaseExists =
-                    allPaths.some((p) => p.path === childBase) ||
-                    derivedBasePaths.some((p) => p.path === childBase);
-                  if (!childBaseExists) {
+                  // 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
-                  const parentBaseExists =
-                    allPaths.some((p) => p.path === parentBase) ||
-                    derivedBasePaths.some((p) => p.path === parentBase);
-                  if (!parentBaseExists) {
+                  // 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);
                   }
                 }
               }
@@ -537,6 +722,26 @@ export default function mergeInDependentDataStructure({
         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) {
           const dataStructures =
             equivalentRoot.function &&
@@ -584,21 +789,20 @@ export default function mergeInDependentDataStructure({
           }
 
           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);
-                }
-              }
-
+            // 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) {
               if (schemaPathParts.length < pathParts.length) continue;
 
               // Check if all path parts match (allowing function call variants)
@@ -667,13 +871,29 @@ export default function mergeInDependentDataStructure({
                     schemaPathParts.slice(matchedUpToIndex),
                   );
 
-                  entry.equivalentPostfixes[postfix] = entry
-                    .equivalentPostfixes[postfix]
-                    ? bestValueFromOptions([
-                        entry.equivalentPostfixes[postfix],
-                        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,
+                      },
+                    });
+                  }
                 }
               }
             }
@@ -710,10 +930,17 @@ export default function mergeInDependentDataStructure({
         const entry = findOrCreateEquivalentSchemaPathsEntry([
           { path: translatedBasePath, functionName: functionName },
         ]);
-        entry.equivalentRoots.push({
+        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) {
@@ -733,14 +960,14 @@ export default function mergeInDependentDataStructure({
           const postfix = joinParenthesesAndArrays(
             schemaPathParts.slice(basePathParts.length),
           );
-          entry.equivalentPostfixes[postfix] = entry.equivalentPostfixes[
-            postfix
-          ]
+          const newValue = entry.equivalentPostfixes[postfix]
             ? bestValueFromOptions([
                 entry.equivalentPostfixes[postfix],
                 dataStructure.returnValueSchema[schemaPath],
               ])
             : dataStructure.returnValueSchema[schemaPath];
+
+          entry.equivalentPostfixes[postfix] = newValue;
         }
       }
     }
@@ -795,6 +1022,10 @@ export default function mergeInDependentDataStructure({
       equivalentRootFunction: (typeof equivalentSchemaPaths)[0]['equivalentRoots'][0]['function'],
     ) => {
       let postfix: string | undefined;
+
+      // Get the signature index we're looking for (if any)
+      const lookingForSignatureIndex = extractSignatureIndex(schemaSubPath);
+
       const equivalentEntry = mergedEquivalentSchemaPaths.find((esp) =>
         esp.equivalentRoots.some((er) => {
           if (
@@ -807,6 +1038,35 @@ export default function mergeInDependentDataStructure({
           }
 
           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;
+              }
+            }
+
             postfix = er.postfix;
             return true;
           }
@@ -940,6 +1200,10 @@ export default function mergeInDependentDataStructure({
 
   equivalentSchemaPaths = mergeAllEquivalentSchemaPaths();
 
+  // 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 }>();
+
   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.
@@ -1037,6 +1301,15 @@ export default function mergeInDependentDataStructure({
         // 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;
         }
 
@@ -1060,6 +1333,16 @@ export default function mergeInDependentDataStructure({
             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
@@ -1068,17 +1351,45 @@ export default function mergeInDependentDataStructure({
             !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;
       }
 
-      cleanSchema(schema);
+      schemasToClean.add(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).
@@ -1197,6 +1508,14 @@ export default function mergeInDependentDataStructure({
           `${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;
     }
 
@@ -1281,7 +1600,10 @@ export default function mergeInDependentDataStructure({
       }
     }
 
-    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),
@@ -1358,7 +1680,10 @@ export default function mergeInDependentDataStructure({
       }
     }
 
-    cleanSchema(depSchema.returnValueSchema);
+    cleanSchema(depSchema.returnValueSchema, {
+      stage: 'afterSignatureRequirementsMerge',
+      dependency: dependency.name,
+    });
   }
 
   // Process the input dependencySchemas FIRST (before child dependentAnalyses).
@@ -1399,7 +1724,11 @@ export default function mergeInDependentDataStructure({
         // 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);
+        cleanSchema(depSchema.returnValueSchema, {
+          stage: 'afterDependencySchemaCopy',
+          filePath,
+          dependency: name,
+        });
       }
 
       // TYPE REFINEMENT: Check if dependentAnalyses has a more specific type for this dependency.
@@ -1470,7 +1799,12 @@ export default function mergeInDependentDataStructure({
                 srcSchema.returnValueSchema[path];
             }
           }
-          cleanSchema(variantSchema.returnValueSchema);
+          cleanSchema(variantSchema.returnValueSchema, {
+            stage: 'afterTypeVariantCopy',
+            filePath,
+            dependency: name,
+            variant,
+          });
         }
       }
     }

package/analyzer-template/packages/analyze/src/lib/index.ts

@@ -4,3 +4,4 @@ export { type FunctionDependenciesMap } from './asts/sourceFiles/getPseudoFile';
 export * as asts from './asts/index';
 export * as projects from './projects/index';
 export * as types from './types';
+export { transformationTracer } from './files/scenarios/TransformationTracer';