diff --git a/README.md b/README.md
index 3045b47..6db7a00 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,6 @@
 * Change prompt CLI inputs to `[PROMPT] [--] [ARGS]`. If `PROMPT` does not
   contain any spaces or `ARGS` (or `--`) is present, it will be interpreted as a
   template name. Otherwise an inline prompt.
-* Only include files that the bot has written in draft commits.
 * Add `--generate` timeout option.
 * Add a compatibility OpenAI bot version which does not use threads, so that it
   can be used with tools only. Gemini only supports the latter.
diff --git a/src/git_draft/drafter.py b/src/git_draft/drafter.py
index 29df65a..ad29375 100644
--- a/src/git_draft/drafter.py
+++ b/src/git_draft/drafter.py
@@ -59,6 +59,7 @@ class _Toolbox(Toolbox):
     def __init__(self, repo: git.Repo, hook: OperationHook | None) -> None:
         super().__init__(hook)
         self._repo = repo
+        self._written = set[str]()
 
     @override
     def _list(self) -> Sequence[PurePosixPath]:
@@ -72,17 +73,28 @@ def _read(self, path: PurePosixPath) -> str:
 
     @override
     def _write(self, path: PurePosixPath, contents: str) -> None:
+        self._written.add(str(path))
         # Update the index without touching the worktree.
         # https://stackoverflow.com/a/25352119
         with tempfile.NamedTemporaryFile(delete_on_close=False) as temp:
             temp.write(contents.encode("utf8"))
             temp.close()
-            sha = self._repo.git.hash_object("-w", "--path", path, temp.name)
+            sha = self._repo.git.hash_object("-w", temp.name, path=path)
             mode = 644  # TODO: Read from original file if it exists.
             self._repo.git.update_index(
-                "--add", "--cacheinfo", f"{mode},{sha},{path}"
+                f"{mode},{sha},{path}", add=True, cacheinfo=True
             )
 
+    def update_index(self) -> None:
+        diff = self._repo.git.diff(name_only=True, cached=True)
+        untouched = [
+            path
+            for path in diff.splitlines()
+            if path and path not in self._written
+        ]
+        if untouched:
+            self._repo.git.reset("--", *untouched)
+
 
 class Drafter:
     """Draft state orchestrator"""
@@ -151,6 +163,7 @@ def generate_draft(
         action = bot.act(prompt_contents, toolbox)
         end_time = time.perf_counter()
 
+        toolbox.update_index()
         title = action.title
         if not title:
             title = _default_title(prompt_contents)
@@ -197,7 +210,7 @@ def _create_branch(self, sync: bool) -> _Branch:
         origin_branch = self._repo.active_branch.name
         origin_sha = self._repo.commit().hexsha
 
-        self._repo.git.checkout("--detach")
+        self._repo.git.checkout(detach=True)
         sync_sha = self._stage_changes(sync)
         suffix = _Branch.new_suffix()
 
@@ -248,7 +261,7 @@ def _exit_draft(self, apply: bool, delete=False) -> None:
         # We do a small dance to move back to the original branch, keeping the
         # draft branch untouched. See https://stackoverflow.com/a/15993574 for
         # the inspiration.
-        self._repo.git.checkout("--detach")
+        self._repo.git.checkout(detach=True)
         self._repo.git.reset("--mixed" if apply else "--hard", origin_branch)
         self._repo.git.checkout(origin_branch)
 
diff --git a/tests/git_draft/drafter_test.py b/tests/git_draft/drafter_test.py
index 4db31d0..059b044 100644
--- a/tests/git_draft/drafter_test.py
+++ b/tests/git_draft/drafter_test.py
@@ -71,20 +71,29 @@ def _write(self, name: str, contents="") -> None:
     def _commits(self) -> Sequence[git.Commit]:
         return list(self._repo.iter_commits())
 
-    def _list_commit_files(self, ref: str) -> Sequence[str]:
+    def _commit_files(self, ref: str) -> frozenset[str]:
         text = self._repo.git.diff_tree(
             ref, no_commit_id=True, name_only=True, relative=True
         )
-        return text.splitlines()
+        return frozenset(text.splitlines())
 
     def test_generate_draft(self) -> None:
         self._drafter.generate_draft("hello", FakeBot())
         assert len(self._commits()) == 2
 
-    def test_generate_stages_worktree(self) -> None:
-        self._write("marker", "hi")
-        self._drafter.generate_draft("hello", FakeBot())
-        assert "marker" in self._list_commit_files("HEAD")
+    def test_generate_stages_then_resets_worktree(self) -> None:
+        self._write("p1", "a")
+        self._write("p2", "b")
+
+        class CustomBot(Bot):
+            def act(self, prompt: str, toolbox: Toolbox) -> Action:
+                assert toolbox.read_file(PurePosixPath("p1")) == "a"
+                toolbox.write_file(PurePosixPath("p2"), "B")
+                toolbox.write_file(PurePosixPath("p3"), "C")
+                return Action()
+
+        self._drafter.generate_draft("hello", CustomBot())
+        assert self._commit_files("HEAD") == set(["p2", "p3"])
 
     def test_generate_then_discard_draft(self) -> None:
         self._drafter.generate_draft("hello", FakeBot())