diff --git a/apps/server/src/vcs/GitVcsDriver.test.ts b/apps/server/src/vcs/GitVcsDriver.test.ts
index 4df6d0eefc5c..ead9e76ab189 100644
--- a/apps/server/src/vcs/GitVcsDriver.test.ts
+++ b/apps/server/src/vcs/GitVcsDriver.test.ts
@@ -15,6 +15,7 @@ import { ChildProcessSpawner } from "effect/unstable/process";
 import { assert, it } from "@effect/vitest";
 
 import { CheckpointRef, GitCommandError, VcsProcessExitError } from "@t3tools/contracts";
+import { symlinksSupported } from "@t3tools/shared/testing/symlinks";
 import * as ServerConfig from "../config.ts";
 import * as CheckpointStore from "../checkpointing/CheckpointStore.ts";
 import * as ProcessRunner from "../processRunner.ts";
@@ -163,6 +164,91 @@ it.effect("checkpoint capture skips untracked nested repositories without a comm
   }).pipe(Effect.scoped, Effect.provide(GitContractLayer)),
 );
 
+it.effect.skipIf(!symlinksSupported)(
+  "checkpoint capture writes its index into the real git dir when cwd is a symlinked subdirectory",
+  () =>
+    Effect.gen(function* () {
+      const fileSystem = yield* FileSystem.FileSystem;
+      const path = yield* Path.Path;
+      const liveRunner = yield* ProcessRunner.ProcessRunner;
+      const indexFiles: string[] = [];
+      const captureProcess = yield* VcsProcess.make.pipe(
+        Effect.provideService(ProcessRunner.ProcessRunner, {
+          run: (input) => {
+            const indexFile = input.env?.GIT_INDEX_FILE;
+            if (indexFile !== undefined) indexFiles.push(indexFile);
+            return liveRunner.run(input);
+          },
+        }),
+      );
+      const driver = yield* GitVcsDriver.makeVcsDriverShape().pipe(
+        Effect.provideService(VcsProcess.VcsProcess, captureProcess),
+      );
+      const sandbox = yield* fileSystem.makeTempDirectoryScoped({
+        prefix: "t3-checkpoint-symlink-",
+      });
+      const repo = path.join(sandbox, "repo");
+      const subdir = path.join(repo, "sub", "dir");
+      const link = path.join(sandbox, "nest", "link");
+      yield* fileSystem.makeDirectory(subdir, { recursive: true });
+      yield* fileSystem.makeDirectory(path.dirname(link), { recursive: true });
+      yield* fileSystem.symlink(subdir, link);
+      /** Runs git in `cwd` through the checkpoint driver under test. */
+      const git = (cwd: string, args: ReadonlyArray<string>) =>
+        driver.execute({ operation: "checkpoint-test", cwd, args });
+      yield* git(repo, ["init"]);
+      yield* git(repo, ["config", "user.name", "Test"]);
+      yield* git(repo, ["config", "user.email", "test@test.com"]);
+      yield* fileSystem.writeFileString(path.join(repo, "file.txt"), "initial\n");
+      yield* git(repo, ["add", "."]);
+      yield* git(repo, ["commit", "-m", "initial"]);
+      yield* fileSystem.writeFileString(path.join(subdir, "nested.txt"), "from-link\n");
+
+      const realCommonDir = yield* fileSystem.realPath(
+        (yield* git(repo, [
+          "rev-parse",
+          "--path-format=absolute",
+          "--git-common-dir",
+        ])).stdout.trim(),
+      );
+      /**
+       * Checkpoint Git commands must keep the private index in the repository
+       * that owns `cwd`, including when a different repository sits where a
+       * lexical `path.resolve` of the relative common dir would land.
+       */
+      const assertIndexesStayInRealCommonDir = Effect.gen(function* () {
+        assert.isTrue(indexFiles.length > 0);
+        for (const indexFile of indexFiles) {
+          assert.strictEqual(yield* fileSystem.realPath(path.dirname(indexFile)), realCommonDir);
+        }
+      });
+
+      const checkpointRef = CheckpointRef.make("refs/t3/checkpoints/symlink");
+      yield* driver.checkpoints.captureCheckpoint({ cwd: link, checkpointRef });
+      yield* assertIndexesStayInRealCommonDir;
+      assert.strictEqual(
+        (yield* git(repo, ["show", `${checkpointRef}:sub/dir/nested.txt`])).stdout,
+        "from-link\n",
+      );
+
+      indexFiles.length = 0;
+      yield* git(sandbox, ["init", "-b", "decoy-only"]);
+      yield* git(sandbox, ["config", "user.name", "Test"]);
+      yield* git(sandbox, ["config", "user.email", "test@test.com"]);
+      yield* git(sandbox, ["commit", "--allow-empty", "-m", "decoy"]);
+      yield* fileSystem.writeFileString(path.join(subdir, "nested.txt"), "again\n");
+      const decoyRef = CheckpointRef.make("refs/t3/checkpoints/symlink-decoy");
+      yield* driver.checkpoints.captureCheckpoint({ cwd: link, checkpointRef: decoyRef });
+      yield* assertIndexesStayInRealCommonDir;
+      const decoyEntries = yield* fileSystem.readDirectory(path.join(sandbox, ".git"));
+      assert.isFalse(decoyEntries.some((entry) => entry.startsWith("t3-checkpoint-index")));
+      assert.strictEqual(
+        (yield* git(repo, ["show", `${decoyRef}:sub/dir/nested.txt`])).stdout,
+        "again\n",
+      );
+    }).pipe(Effect.scoped, Effect.provide(GitCaptureContractLayer)),
+);
+
 it.effect("checkpoint recovery discovers nested HEAD independently of inherited GIT_DIR", () =>
   Effect.gen(function* () {
     const fs = yield* FileSystem.FileSystem;
diff --git a/apps/server/src/vcs/GitVcsDriver.ts b/apps/server/src/vcs/GitVcsDriver.ts
index f450eef0dc24..d220c1f59f19 100644
--- a/apps/server/src/vcs/GitVcsDriver.ts
+++ b/apps/server/src/vcs/GitVcsDriver.ts
@@ -753,12 +753,23 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
       }),
     );
 
+  /**
+   * Absolute path of the repository's common git directory, where checkpoint
+   * capture places its private index.
+   *
+   * A relative `--git-common-dir` is computed from Git's physical working
+   * directory. Joining it with `path.resolve` applies `..` to the project path
+   * string, so a symlink into a repository subdirectory climbs out of the
+   * symlink and `GIT_INDEX_FILE` points at a directory that does not exist
+   * (exit 128). `--path-format=absolute` is the same request already used for
+   * `--git-path index`.
+   */
   const resolveGitCommonDir = (cwd: string) =>
     Effect.gen(function* () {
       const result = yield* execute({
         operation: "GitVcsDriver.checkpoints.resolveGitCommonDir",
         cwd,
-        args: ["rev-parse", "--git-common-dir"],
+        args: ["rev-parse", "--path-format=absolute", "--git-common-dir"],
       });
       const gitCommonDir = result.stdout.trim();
       return path.isAbsolute(gitCommonDir) ? gitCommonDir : path.resolve(cwd, gitCommonDir);
diff --git a/apps/server/src/vcs/GitVcsDriverCore.test.ts b/apps/server/src/vcs/GitVcsDriverCore.test.ts
index 98dec86522de..f6acda649552 100644
--- a/apps/server/src/vcs/GitVcsDriverCore.test.ts
+++ b/apps/server/src/vcs/GitVcsDriverCore.test.ts
@@ -28,6 +28,7 @@ import {
   type ReviewDiffFileContentsInput,
   type WorktreeSubmodules,
 } from "@t3tools/contracts";
+import { symlinksSupported } from "@t3tools/shared/testing/symlinks";
 import { ServerConfig } from "../config.ts";
 import { gitCommandDuration } from "../observability/Metrics.ts";
 import {
@@ -334,7 +335,7 @@ it.effect("uses stable diagnostics for every parsed non-repository command", ()
       { args: ["rev-parse", "--git-path", "index"], lcAll: "C" },
       { args: ["status", "--porcelain=2", "--branch"], lcAll: "C" },
       { args: ["rev-parse", "--abbrev-ref", "HEAD"], lcAll: "C" },
-      { args: ["rev-parse", "--git-common-dir"], lcAll: "C" },
+      { args: ["rev-parse", "--path-format=absolute", "--git-common-dir"], lcAll: "C" },
     ]);
   }).pipe(Effect.provide(layer));
 });
@@ -1688,6 +1689,41 @@ it.layer(TestLayer)("GitVcsDriver core integration", (it) => {
   });
 
   describe("repository status", () => {
+    it.effect.skipIf(!symlinksSupported)(
+      "resolves the common dir through a symlink into a repository subdirectory",
+      () =>
+        Effect.gen(function* () {
+          const fileSystem = yield* FileSystem.FileSystem;
+          const pathService = yield* Path.Path;
+          const sandbox = yield* makeTmpDir("git-symlink-subdir-");
+          const repo = pathService.join(sandbox, "repo");
+          const link = pathService.join(sandbox, "nest", "link");
+          yield* fileSystem.makeDirectory(pathService.join(repo, "sub", "dir"), {
+            recursive: true,
+          });
+          yield* fileSystem.makeDirectory(pathService.dirname(link), { recursive: true });
+          yield* fileSystem.symlink(pathService.join(repo, "sub", "dir"), link);
+          yield* initRepoWithCommit(repo);
+          yield* git(repo, ["checkout", "-b", "real-only"]);
+
+          const driver = yield* GitVcsDriver.GitVcsDriver;
+          const refsBeforeDecoy = yield* driver.listRefs({ cwd: link, refresh: true });
+          assert.isTrue(refsBeforeDecoy.isRepo);
+          assert.isTrue(refsBeforeDecoy.refs.some((ref) => ref.name === "real-only"));
+
+          // The lexical join of the symlink with ../../.git is sandbox/.git.
+          // That directory must not be treated as this repository.
+          yield* git(sandbox, ["init", "-b", "decoy-only"]);
+          yield* git(sandbox, ["config", "user.email", "test@test.com"]);
+          yield* git(sandbox, ["config", "user.name", "Test"]);
+          yield* git(sandbox, ["commit", "--allow-empty", "-m", "decoy"]);
+
+          const refsAfterDecoy = yield* driver.listRefs({ cwd: link, refresh: true });
+          assert.isTrue(refsAfterDecoy.refs.some((ref) => ref.name === "real-only"));
+          assert.isFalse(refsAfterDecoy.refs.some((ref) => ref.name === "decoy-only"));
+        }),
+    );
+
     it.effect("reports non-repository directories without failing", () =>
       Effect.gen(function* () {
         const cwd = yield* makeTmpDir();
diff --git a/apps/server/src/vcs/GitVcsDriverCore.ts b/apps/server/src/vcs/GitVcsDriverCore.ts
index 5fbae919c258..23ea51226db3 100644
--- a/apps/server/src/vcs/GitVcsDriverCore.ts
+++ b/apps/server/src/vcs/GitVcsDriverCore.ts
@@ -1142,13 +1142,23 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
     ).pipe(Effect.asVoid);
   };
 
+  /**
+   * Resolves the common git directory, worktree root, and current branch.
+   *
+   * `--git-common-dir` is requested with `--path-format=absolute` because a
+   * relative answer is computed from Git's physical working directory.
+   * `path.resolve` would apply `..` to a symlinked project path and climb out
+   * of a symlink that points at a repository subdirectory. `realPath` still
+   * runs afterward so Windows 8.3 short names collapse to one directory.
+   */
   const resolveRepositoryPathsUncached = Effect.fn("resolveRepositoryPathsUncached")(function* (
     cwd: string,
   ) {
+    const gitCommonDirArgs = ["rev-parse", "--path-format=absolute", "--git-common-dir"] as const;
     const commonDirResult = yield* executeGitWithStableDiagnostics(
       "GitVcsDriver.resolveRepositoryPaths.commonDir",
       cwd,
-      ["rev-parse", "--git-common-dir"],
+      gitCommonDirArgs,
       {
         timeoutMs: 5_000,
         allowNonZeroExit: true,
@@ -1163,7 +1173,7 @@ export const makeGitVcsDriverCore = Effect.fn("makeGitVcsDriverCore")(function*
         ...gitCommandContext({
           operation: "GitVcsDriver.resolveRepositoryPaths.commonDir",
           cwd,
-          args: ["rev-parse", "--git-common-dir"],
+          args: gitCommonDirArgs,
         }),
         detail: "Failed to resolve the Git common directory.",
         exitCode: commonDirResult.exitCode,