diff --git a/src/application/ReferenceSourceGitDirectory.ts b/src/application/ReferenceSourceGitDirectory.ts
index a2543d51cf..0cb9257cc8 100644
--- a/src/application/ReferenceSourceGitDirectory.ts
+++ b/src/application/ReferenceSourceGitDirectory.ts
@@ -41,20 +41,20 @@ export const locateReferenceSourceGitDirectory = async (
     // Derived joins and the Git library normalize paths lexically. Admit the
     // physical directory first, while the source pointer stays in its file.
     const gitDirectory = await realpath(selectedGitDirectory);
-    let commonDirectory = gitDirectory;
+    let common: string | undefined;
     try {
-      const common = (await readText(join(gitDirectory, "commondir"))).replace(
+      common = (await readText(join(gitDirectory, "commondir"))).replace(
         /\r?\n$/u,
         "",
       );
-      if (common.length === 0)
-        throw new Error("Invalid Git common-directory pointer");
-      commonDirectory = await realpath(
-        absoluteCallerPath(common, { cwd: gitDirectory }),
-      );
     } catch (cause: unknown) {
       if (!hasCode(cause, "ENOENT")) throw cause;
     }
+    if (common === "") throw new Error("Invalid Git common-directory pointer");
+    const commonDirectory =
+      common === undefined
+        ? gitDirectory
+        : await realpath(absoluteCallerPath(common, { cwd: gitDirectory }));
     return { repository, gitDirectory, commonDirectory };
   }
 };
diff --git a/src/reference/ReferenceSourceReader.ts b/src/reference/ReferenceSourceReader.ts
index ab3afc3a76..3d6577e4d1 100644
--- a/src/reference/ReferenceSourceReader.ts
+++ b/src/reference/ReferenceSourceReader.ts
@@ -91,6 +91,13 @@ const readSource = async (
     bytesRead: state.bytesRead,
     limitations: [PATH_RACE_LIMITATION],
   };
+  if (traversal.ok && state.rootFailure?.code === "io")
+    return err({
+      tag: "reference-source-reader",
+      code: "io",
+      message: state.rootFailure.message,
+      partial: read,
+    });
   return traversal.ok ? ok(read) : err({ ...traversal.error, partial: read });
 };
 
diff --git a/tests/boundary/filesystem/referenceSourceIgnorePolicy.test.ts b/tests/boundary/filesystem/referenceSourceIgnorePolicy.test.ts
index 565ddf9088..e9311d574b 100644
--- a/tests/boundary/filesystem/referenceSourceIgnorePolicy.test.ts
+++ b/tests/boundary/filesystem/referenceSourceIgnorePolicy.test.ts
@@ -155,3 +155,20 @@ it.skipIf(process.platform === "win32")(
     expect(graph.vcs).toMatchObject({ kind: "git", head: intendedHead });
   },
 );
+
+it("keeps a present but unresolved Git common-directory pointer from selecting private decoy configuration", async () => {
+  const root = await createTestTempDirectory("rea-reference-common-missing-");
+  await mkdir(join(root, ".git"));
+  await writeFile(join(root, ".git", "HEAD"), `${"1".repeat(40)}\n`);
+  await writeFile(join(root, ".git", "config"), "[core]\nignorecase = true\n");
+  await writeFile(join(root, ".git", "commondir"), "../missing-common\n");
+  const result = await importReferenceSource({
+    root,
+    caller: "ignore-policy-test",
+    policy: { secretPatterns: [] },
+  });
+  expect(result).toMatchObject({
+    ok: false,
+    error: { code: "io", message: expect.stringContaining("missing-common") },
+  });
+});
diff --git a/tests/boundary/filesystem/referenceSourceUnreadableDirectories.test.ts b/tests/boundary/filesystem/referenceSourceUnreadableDirectories.test.ts
index cc5b689e49..8747c81d8e 100644
--- a/tests/boundary/filesystem/referenceSourceUnreadableDirectories.test.ts
+++ b/tests/boundary/filesystem/referenceSourceUnreadableDirectories.test.ts
@@ -20,6 +20,33 @@ const permissionChecksUnavailable =
   process.platform === "win32" || process.getuid?.() === 0;
 
 describe("reference source native unreadable directories", () => {
+  it.skipIf(permissionChecksUnavailable)(
+    "retains a root enumeration IO failure as an error and recovers after permission repair",
+    async () => {
+      const root = await createTestTempDirectory("rea-source-unreadable-root-");
+      await writeFile(join(root, "main.txt"), "root bytes");
+      await chmod(root, 0o100);
+      try {
+        const result = await importTree(root);
+        expect(result).toMatchObject({
+          ok: false,
+          error: {
+            code: "io",
+            message: expect.stringContaining("EACCES"),
+            partial: { rootFailure: { code: "io" } },
+          },
+        });
+        if (!result.ok) expect(result.error.message).toContain(root);
+      } finally {
+        await chmod(root, 0o700);
+      }
+      const recovered = await importTree(root);
+      expect(recovered.ok && recovered.value.entries).toContainEqual(
+        expect.objectContaining({ path: "main.txt", content_state: "hashed" }),
+      );
+    },
+  );
+
   it.skipIf(permissionChecksUnavailable).each(["blocked", "src/blocked"])(
     "preserves a partial graph when %s cannot be enumerated",
     async (blocked) => {