diff --git a/apps/server/src/vcs/GitVcsDriver.test.ts b/apps/server/src/vcs/GitVcsDriver.test.ts
index 031055a3b6c..6abddc64165 100644
--- a/apps/server/src/vcs/GitVcsDriver.test.ts
+++ b/apps/server/src/vcs/GitVcsDriver.test.ts
@@ -7,7 +7,7 @@ import * as PlatformError from "effect/PlatformError";
 import { ChildProcessSpawner } from "effect/unstable/process";
 import { assert, it } from "@effect/vitest";
 
-import { GitCommandError } from "@t3tools/contracts";
+import { CheckpointRef, GitCommandError } from "@t3tools/contracts";
 import * as ServerConfig from "../config.ts";
 import * as GitVcsDriver from "./GitVcsDriver.ts";
 import * as VcsProcess from "./VcsProcess.ts";
@@ -65,6 +65,168 @@ runVcsDriverContractSuite<GitVcsDriver.GitVcsDriver, GitContractError>({
   },
 });
 
+const makeCheckpointFixture = Effect.fn("makeCheckpointFixture")(function* (
+  driver: Effect.Success<ReturnType<typeof GitVcsDriver.makeVcsDriverShape>>,
+  cwd: string,
+) {
+  const fileSystem = yield* FileSystem.FileSystem;
+  const path = yield* Path.Path;
+  const git = (args: ReadonlyArray<string>) =>
+    driver.execute({ operation: "checkpoint-test", cwd, args });
+  yield* git(["init"]);
+  yield* git(["config", "user.name", "Test"]);
+  yield* git(["config", "user.email", "test@test.com"]);
+  yield* fileSystem.writeFileString(path.join(cwd, "file.txt"), "initial\n");
+  yield* git(["add", "."]);
+  yield* git(["commit", "-m", "initial"]);
+  const checkpointRef = CheckpointRef.make("refs/t3/checkpoints/test");
+  yield* fileSystem.writeFileString(path.join(cwd, "file.txt"), "staged\n");
+  yield* git(["add", "."]);
+  yield* fileSystem.writeFileString(path.join(cwd, "file.txt"), "unstaged\n");
+  return { git, checkpointRef };
+});
+
+it.effect("checkpoint capture does not rerun clean filters for unchanged indexed files", () =>
+  Effect.gen(function* () {
+    const fileSystem = yield* FileSystem.FileSystem;
+    const path = yield* Path.Path;
+    const driver = yield* GitVcsDriver.makeVcsDriverShape();
+    const cwd = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-checkpoint-cache-" });
+    const { git, checkpointRef } = yield* makeCheckpointFixture(driver, cwd);
+    yield* fileSystem.writeFileString(
+      path.join(cwd, ".gitattributes"),
+      "stable.txt filter=probe\n",
+    );
+    yield* fileSystem.writeFileString(path.join(cwd, "stable.txt"), "unchanged\n");
+    yield* fileSystem.writeFileString(
+      path.join(cwd, ".git", "filter.cjs"),
+      'require("node:fs").appendFileSync(".git/filter-runs", "read\\n"); process.stdin.pipe(process.stdout);',
+    );
+    yield* git(["config", "filter.probe.clean", "node .git/filter.cjs"]);
+    yield* fileSystem.utimes(path.join(cwd, "stable.txt"), 1_700_000_000, 1_700_000_000);
+    yield* git(["add", "."]);
+    yield* git(["commit", "-m", "record stable file"]);
+    yield* fileSystem.writeFileString(path.join(cwd, ".git", "filter-runs"), "");
+    yield* fileSystem.writeFileString(path.join(cwd, "file.txt"), "changed\n");
+    const originalIndex = yield* fileSystem.readFile(path.join(cwd, ".git", "index"));
+
+    yield* driver.checkpoints.captureCheckpoint({ cwd, checkpointRef });
+
+    assert.strictEqual(yield* fileSystem.readFileString(path.join(cwd, ".git", "filter-runs")), "");
+    assert.strictEqual((yield* git(["show", `${checkpointRef}:file.txt`])).stdout, "changed\n");
+    assert.strictEqual((yield* git(["show", `${checkpointRef}:stable.txt`])).stdout, "unchanged\n");
+    assert.deepEqual(yield* fileSystem.readFile(path.join(cwd, ".git", "index")), originalIndex);
+  }).pipe(Effect.scoped, Effect.provide(GitContractLayer)),
+);
+
+for (const nested of [false, true]) {
+  for (const indexMode of ["normal", "flags", "split"] as const) {
+    it.effect(
+      `checkpoint index reuse preserves two turns (nested=${nested}, index=${indexMode})`,
+      () =>
+        Effect.gen(function* () {
+          const fileSystem = yield* FileSystem.FileSystem;
+          const path = yield* Path.Path;
+          const driver = yield* GitVcsDriver.makeVcsDriverShape();
+          const cwd = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-checkpoint-turns-" });
+          const { git } = yield* makeCheckpointFixture(driver, cwd);
+          const write = (name: string, contents: string) =>
+            fileSystem.writeFileString(path.join(cwd, name), contents);
+          yield* fileSystem.makeDirectory(path.join(cwd, "scope"));
+          for (const name of [
+            "scope/staged",
+            "scope/deleted",
+            "scope/assumed",
+            "scope/skipped",
+            "outside",
+          ]) {
+            yield* write(name, "original\n");
+          }
+          yield* git(["add", "."]);
+          yield* git(["commit", "-m", "initial scoped files"]);
+          yield* write("scope/staged", "staged\n");
+          yield* write("scope/new-deleted", "staged then deleted\n");
+          yield* write("outside", "staged outside\n");
+          yield* git(["add", "."]);
+          if (indexMode === "flags") {
+            yield* git(["update-index", "--assume-unchanged", "scope/assumed"]);
+            yield* git(["update-index", "--skip-worktree", "scope/skipped"]);
+          }
+          if (indexMode === "split") {
+            yield* git(["update-index", "--split-index"]);
+          }
+          const originalIndex = yield* fileSystem.readFile(path.join(cwd, ".git", "index"));
+          for (const name of ["scope/staged", "scope/assumed", "scope/skipped", "outside"]) {
+            yield* write(name, "working\n");
+          }
+          yield* write("scope/new", "first\n");
+          yield* fileSystem.remove(path.join(cwd, "scope/deleted"));
+          yield* fileSystem.remove(path.join(cwd, "scope/new-deleted"));
+          const captureCwd = nested ? path.join(cwd, "scope") : cwd;
+          const first = CheckpointRef.make("refs/t3/checkpoints/turns/1");
+          const second = CheckpointRef.make("refs/t3/checkpoints/turns/2");
+          yield* driver.checkpoints.captureCheckpoint({ cwd: captureCwd, checkpointRef: first });
+          for (const name of ["scope/staged", "scope/assumed", "scope/skipped"]) {
+            assert.strictEqual((yield* git(["show", `${first}:${name}`])).stdout, "working\n");
+          }
+          assert.strictEqual(
+            (yield* git(["show", `${first}:outside`])).stdout,
+            nested ? "original\n" : "working\n",
+          );
+          const files = (yield* git(["ls-tree", "-r", "--name-only", first])).stdout.split("\n");
+          assert.notInclude(files, "scope/deleted");
+          assert.notInclude(files, "scope/new-deleted");
+          assert.include(files, "scope/new");
+
+          yield* write("scope/staged", "second\n");
+          yield* fileSystem.remove(path.join(cwd, "scope/new"));
+          yield* write("scope/second", "added in second turn\n");
+          yield* driver.checkpoints.captureCheckpoint({ cwd: captureCwd, checkpointRef: second });
+          assert.strictEqual(
+            (yield* git(["diff", "--name-only", first, second])).stdout,
+            "scope/new\nscope/second\nscope/staged\n",
+          );
+          assert.strictEqual((yield* git(["show", `${second}:scope/staged`])).stdout, "second\n");
+          assert.strictEqual(
+            (yield* git(["show", `${second}:scope/second`])).stdout,
+            "added in second turn\n",
+          );
+          assert.deepEqual(
+            yield* fileSystem.readFile(path.join(cwd, ".git", "index")),
+            originalIndex,
+          );
+        }).pipe(Effect.scoped, Effect.provide(GitContractLayer)),
+    );
+  }
+}
+
+for (const indexState of ["missing", "invalid"] as const) {
+  it.effect(`checkpoint capture falls back when the user index is ${indexState}`, () =>
+    Effect.gen(function* () {
+      const fileSystem = yield* FileSystem.FileSystem;
+      const path = yield* Path.Path;
+      const driver = yield* GitVcsDriver.makeVcsDriverShape();
+      const cwd = yield* fileSystem.makeTempDirectoryScoped({ prefix: "t3-checkpoint-index-" });
+      const { git, checkpointRef } = yield* makeCheckpointFixture(driver, cwd);
+      const indexPath = path.join(cwd, ".git", "index");
+      if (indexState === "missing") {
+        yield* fileSystem.remove(indexPath);
+      } else {
+        yield* fileSystem.writeFileString(indexPath, "invalid index");
+      }
+
+      yield* driver.checkpoints.captureCheckpoint({ cwd, checkpointRef });
+
+      assert.strictEqual((yield* git(["show", `${checkpointRef}:file.txt`])).stdout, "unstaged\n");
+      if (indexState === "missing") {
+        assert.isFalse(yield* fileSystem.exists(indexPath));
+      } else {
+        assert.strictEqual(yield* fileSystem.readFileString(indexPath), "invalid index");
+      }
+    }).pipe(Effect.scoped, Effect.provide(GitContractLayer)),
+  );
+}
+
 it.effect("GitVcsDriver forwards execute env to the VCS process", () => {
   let observedEnv: NodeJS.ProcessEnv | undefined;
   let observedAppendTruncationMarker: boolean | undefined;
diff --git a/apps/server/src/vcs/GitVcsDriver.ts b/apps/server/src/vcs/GitVcsDriver.ts
index f1e48a24d6f..3426b193145 100644
--- a/apps/server/src/vcs/GitVcsDriver.ts
+++ b/apps/server/src/vcs/GitVcsDriver.ts
@@ -735,12 +735,38 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
       yield* Effect.gen(function* () {
         const headExists = yield* hasHeadCommit(input.cwd);
         if (headExists) {
-          yield* execute({
-            operation,
-            cwd: input.cwd,
-            args: ["read-tree", "HEAD"],
-            env: commitEnv,
-          });
+          const reusedIndex = yield* Effect.gen(function* () {
+            const indexPath = yield* execute({
+              operation,
+              cwd: input.cwd,
+              args: ["rev-parse", "--path-format=absolute", "--git-path", "index"],
+            });
+            yield* fileSystem.copyFile(indexPath.stdout.trim(), tempIndexPath);
+            // Retain stat data only where the copied index already matches HEAD.
+            yield* execute({
+              operation,
+              cwd: input.cwd,
+              args: ["-c", "core.fsmonitor=false", "read-tree", "--reset", "HEAD"],
+              env: commitEnv,
+            });
+            const entries = yield* execute({
+              operation,
+              cwd: input.cwd,
+              args: ["ls-files", "-v"],
+              env: commitEnv,
+              maxOutputBytes: WORKSPACE_FILES_MAX_OUTPUT_BYTES,
+            });
+            // A fresh index must still capture assume-unchanged/skip-worktree files.
+            return !entries.stdoutTruncated && !/^[a-zS] /m.test(entries.stdout);
+          }).pipe(Effect.orElseSucceed(() => false));
+          if (!reusedIndex) {
+            yield* execute({
+              operation,
+              cwd: input.cwd,
+              args: ["read-tree", "HEAD"],
+              env: commitEnv,
+            });
+          }
         }
 
         yield* execute({