fix(reference): preserve distinct parse failures

src/application/ReferenceSourceImport.ts

@@ -1,6 +1,7 @@
 import { isSecretLikePath } from "../domain/referenceSourceClassification.js";
 import {
   createHistoricalSourceGraph,
+  historicalSourceParseFailureKey,
   type HistoricalSourceGraph,
   type HistoricalSourceGraphInput,
 } from "../domain/referenceSourceGraph.js";
@@ -205,16 +206,20 @@ export const importReferenceSource = async (
 
   const uniqueRelationships = deduplicateRelationships(relationships);
   const uniqueFailures = [...parseFailures]
-    .sort((left, right) => {
-      const byPath = byCodePoint(left.path, right.path);
-      if (byPath !== 0) return byPath;
-      return byCodePoint(left.parser, right.parser);
-    })
+    .sort((left, right) =>
+      byCodePoint(
+        historicalSourceParseFailureKey(left),
+        historicalSourceParseFailureKey(right),
+      ),
+    )
     .filter((value, index, array) => {
       if (index === 0) return true;
       const previous = array[index - 1];
       if (previous === undefined) return true;
-      return value.path !== previous.path || value.parser !== previous.parser;
+      return (
+        historicalSourceParseFailureKey(value) !==
+        historicalSourceParseFailureKey(previous)
+      );
     });
 
   const sortedEntries = [...entries].sort((left, right) =>

src/domain/referenceSourceGraph.ts

@@ -225,6 +225,11 @@ export type HistoricalSourceManifest = z.infer<
   typeof historicalSourceManifestBaseSchema
 >;
 
+/** Stable identity used to sort and deduplicate source parse failures. */
+export const historicalSourceParseFailureKey = (
+  failure: HistoricalSourceGraphInput["parse_failures"][number],
+): string => `${failure.path}\u0000${failure.parser}\u0000${failure.reason}`;
+
 const canonicalJson = (value: unknown): string => {
   const serialized = canonicalize(value);
   if (serialized === undefined)
@@ -400,7 +405,7 @@ function checkGraphInvariants(
     context,
   );
   checkSortedUnique(
-    graph.parse_failures.map(({ path, parser }) => `${path}\u0000${parser}`),
+    graph.parse_failures.map(historicalSourceParseFailureKey),
     "parse_failures",
     context,
   );

tests/referenceSourceGraph.test.ts

@@ -5,6 +5,7 @@ import {
   createHistoricalSourceGraph,
   createHistoricalSourceManifest,
   historicalSourceGraphSchema,
+  historicalSourceParseFailureKey,
   parseHistoricalSourceGraph,
   parseHistoricalSourceManifest,
   type HistoricalSourceGraphInput,
@@ -192,6 +193,29 @@ describe("historical source graph", () => {
       ).toThrow(/Complete inventory/u);
   });
 
+  it("keeps distinct parse failure reasons for the same path and parser", () => {
+    const input = graphInput();
+    const malformed = {
+      path: "src/main.ts",
+      parser: "typescript",
+      reason: "Malformed input",
+    };
+    const unexpected = {
+      path: "src/main.ts",
+      parser: "typescript",
+      reason: "Unexpected token",
+    };
+    input.inventory_state = "partial";
+    input.parse_failures = [malformed, unexpected];
+
+    expect(createHistoricalSourceGraph(input).parse_failures).toEqual(
+      input.parse_failures,
+    );
+    expect(historicalSourceParseFailureKey(malformed)).not.toBe(
+      historicalSourceParseFailureKey(unexpected),
+    );
+  });
+
   it("rejects strict unknown fields, invalid VCS, dangling internal edges, and false manifests", () => {
     expect(() =>
       createHistoricalSourceGraph({ ...graphInput(), surprise: true }),