diff --git a/src/application/ReferenceSourceImportTypes.ts b/src/application/ReferenceSourceImportTypes.ts
index d9c2324b74..34ccdbd24e 100644
--- a/src/application/ReferenceSourceImportTypes.ts
+++ b/src/application/ReferenceSourceImportTypes.ts
@@ -125,6 +125,8 @@ export interface ReferenceSourceImportOptions {
 export const DEFAULT_REFERENCE_SOURCE_IGNORE_PATTERNS = [
   ".git/",
   ".git/hooks/",
+  // Match pointer files after directory rules to preserve their provenance.
+  ".git",
   "node_modules/",
   "dist/",
   "build/",
diff --git a/tests/boundary/filesystem/referenceSourceGitMetadataExclusion.test.ts b/tests/boundary/filesystem/referenceSourceGitMetadataExclusion.test.ts
new file mode 100644
index 0000000000..1f072bd554
--- /dev/null
+++ b/tests/boundary/filesystem/referenceSourceGitMetadataExclusion.test.ts
@@ -0,0 +1,208 @@
+import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import ignore from "ignore";
+import { describe, expect, it } from "vitest";
+import { DEFAULT_REFERENCE_SOURCE_IGNORE_PATTERNS } from "../../../src/application/ReferenceSourceImportTypes.js";
+import { createHistoricalSourceManifest } from "../../../src/domain/referenceSourceGraph.js";
+import { execFileOutput } from "../../../src/process/ExecFileOutput.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { importReferenceSource } from "../../support/referenceSourceResourceScope.js";
+
+const importTree = async (
+  root: string,
+  secretPatterns: readonly string[] = [],
+  excludePaths: readonly string[] = [],
+) => {
+  const result = await importReferenceSource({
+    root,
+    caller: "git-metadata-test",
+    policy: { secretPatterns },
+    excludePaths,
+  });
+  if (!result.ok) throw result.error;
+  return result.value;
+};
+
+const fixtureGit = (
+  directory: string,
+  configuration: string,
+  args: readonly string[],
+) =>
+  execFileOutput(
+    "git",
+    ["-c", `core.hooksPath=${join(configuration, "no-hooks")}`, ...args],
+    {
+      cwd: directory,
+      env: {
+        ...Object.fromEntries(
+          Object.entries(process.env).filter(
+            ([name]) => !name.toUpperCase().startsWith("GIT_"),
+          ),
+        ),
+        GIT_CONFIG_GLOBAL: join(configuration, "gitconfig"),
+        GIT_CONFIG_NOSYSTEM: "1",
+        GIT_TEMPLATE_DIR: join(configuration, "no-template"),
+      },
+    },
+  );
+
+it("excludes Git metadata files and directories without broadening directory-only defaults", () => {
+  const matcher = ignore().add([...DEFAULT_REFERENCE_SOURCE_IGNORE_PATTERNS]);
+  for (const path of [".git", ".git/", "nested/.git", "nested/.git/"])
+    expect(matcher.ignores(path), path).toBe(true);
+  for (const path of [".gitignore", ".github", ".gitkeep", "dist"])
+    expect(matcher.ignores(path), path).toBe(false);
+  expect(matcher.ignores("dist/")).toBe(true);
+  expect(matcher.test(".git").rule?.pattern).toBe(".git");
+  expect(matcher.test(".git/").rule?.pattern).toBe(".git/");
+});
+
+describe.skipIf(process.platform === "win32")(
+  "reference source Git metadata exclusions",
+  () => {
+    it("keeps linked-worktree identities stable while retaining HEAD and ordinary-checkout provenance", async () => {
+      const root = await createTestTempDirectory("rea-reference-git-metadata-");
+      const repository = join(root, "repository");
+      await Promise.all([
+        mkdir(join(root, "no-hooks")),
+        mkdir(join(root, "no-template")),
+        writeFile(join(root, "gitconfig"), ""),
+      ]);
+      await mkdir(join(repository, "src"), { recursive: true });
+      await writeFile(
+        join(repository, "src", "main.js"),
+        "export const value = 7;\n",
+      );
+      await writeFile(join(repository, ".gitignore"), "*.log\n");
+      const git = (...args: string[]) => fixtureGit(repository, root, args);
+      await git("init", "--initial-branch=main");
+      await git("add", ".gitignore", "src/main.js");
+      await git(
+        "-c",
+        "user.name=REA fixture",
+        "-c",
+        "user.email=fixture@example.invalid",
+        "-c",
+        "commit.gpgsign=false",
+        "commit",
+        "-m",
+        "fixture",
+      );
+      const head = (await git("rev-parse", "HEAD")).stdout.trim();
+      const leftRoot = join(root, "left");
+      const rightRoot = join(root, "right");
+      for (const worktree of [leftRoot, rightRoot]) {
+        await git("worktree", "add", "--detach", worktree, head);
+        expect(
+          (await fixtureGit(worktree, root, ["status", "--porcelain"])).stdout,
+        ).toBe("");
+      }
+      expect(await readFile(join(leftRoot, ".git"), "utf8")).not.toBe(
+        await readFile(join(rightRoot, ".git"), "utf8"),
+      );
+      const importSelectedTree = async (source: string) => {
+        const graph = await importTree(source);
+        expect(graph.vcs).toEqual({ kind: "git", head, dirty: null });
+        expect(
+          graph.entries
+            .filter(({ kind }) => kind === "file")
+            .map(({ path }) => path),
+        ).toEqual([".gitignore", "src/main.js"]);
+        expect(
+          graph.entries.some(
+            ({ path }) => path === ".git" || path.startsWith(".git/"),
+          ),
+        ).toBe(false);
+        return graph;
+      };
+      const left = await importSelectedTree(leftRoot);
+      const right = await importSelectedTree(rightRoot);
+      const repeated = await importSelectedTree(leftRoot);
+      expect(createHistoricalSourceManifest(left)).toEqual(
+        createHistoricalSourceManifest(right),
+      );
+      expect(createHistoricalSourceManifest(repeated)).toEqual(
+        createHistoricalSourceManifest(left),
+      );
+      for (const graph of [left, right])
+        expect(graph.exclusions).toEqual([
+          {
+            path: ".git",
+            entry_kind: "file",
+            reason: "default-ignored",
+            pattern: ".git",
+          },
+        ]);
+      const ordinary = await importSelectedTree(repository);
+      expect(ordinary.exclusions).toEqual([
+        {
+          path: ".git",
+          entry_kind: "directory",
+          reason: "default-ignored",
+          pattern: ".git/",
+        },
+      ]);
+    });
+
+    it.each(["file", "directory"] as const)(
+      "prunes nested .git %s metadata and preserves configured-secret precedence",
+      async (kind) => {
+        const root = await createTestTempDirectory("rea-reference-nested-git-");
+        const nested = join(root, "nested");
+        await mkdir(nested);
+        if (kind === "file")
+          await writeFile(
+            join(nested, ".git"),
+            "gitdir: /checkout-specific/metadata\n",
+          );
+        else {
+          await mkdir(join(nested, ".git", "hooks"), { recursive: true });
+          await writeFile(
+            join(nested, ".git", "hooks", "pre-commit"),
+            "metadata\n",
+          );
+        }
+        for (const name of [
+          ".gitignore",
+          ".github",
+          ".gitkeep",
+          "dist",
+          "source.js",
+        ])
+          await writeFile(join(nested, name), "");
+        for (const secretPatterns of [[], [".git"]]) {
+          const graph = await importTree(
+            root,
+            secretPatterns,
+            secretPatterns.length === 0 ? [] : ["!.git"],
+          );
+          expect(graph.exclusions).toEqual([
+            {
+              path: "nested/.git",
+              entry_kind: kind,
+              reason:
+                secretPatterns.length === 0
+                  ? "default-ignored"
+                  : "configured-secret",
+              pattern:
+                secretPatterns.length === 0 && kind === "directory"
+                  ? ".git/"
+                  : ".git",
+            },
+          ]);
+          expect(
+            graph.entries
+              .filter(({ kind }) => kind === "file")
+              .map(({ path }) => path),
+          ).toEqual([
+            "nested/.github",
+            "nested/.gitignore",
+            "nested/.gitkeep",
+            "nested/dist",
+            "nested/source.js",
+          ]);
+        }
+      },
+    );
+  },
+);