fix(gitstore): detect rapid same-size rewrites

nanobot/utils/gitstore.py

@@ -133,12 +133,13 @@ class GitStore:
         try:
             from dulwich import porcelain
 
-            # .gitignore excludes everything except tracked files,
+            # Stage first so Dulwich refreshes the content hashes.  A status
-            # so any staged/unstaged change must be in our files.
+            # check can miss rapid same-size rewrites when the filesystem also
+            # preserves the file's mtime.
+            porcelain.add(str(self._workspace), paths=self._staging_paths(*self._tracked_files))
             st = porcelain.status(str(self._workspace))
-            unstaged = cast(list[object], st.unstaged)
             staged = cast(dict[object, list[object]], st.staged)
-            if not unstaged and not any(staged.values()):
+            if not any(staged.values()):
                 return None
 
             message_value = cast(object, message)
@@ -147,7 +148,6 @@ class GitStore:
                 if isinstance(message_value, str)
                 else cast(bytes, message_value)
             )
-            porcelain.add(str(self._workspace), paths=self._staging_paths(*self._tracked_files))
             sha_bytes = porcelain.commit(
                 str(self._workspace),
                 message=msg_bytes,

tests/agent/test_git_store.py

@@ -1,5 +1,6 @@
 """Tests for GitStore — git-backed version control for memory files."""
 
+import os
 from unittest.mock import patch
 
 import pytest
@@ -98,6 +99,18 @@ class TestAutoCommit:
         assert len(commits) == 2
         assert commits[0].sha == sha
 
+    def test_commits_same_size_rewrite_with_unchanged_mtime(self, git_ready):
+        path = git_ready._workspace / "SOUL.md"
+        path.write_text("v1", encoding="utf-8")
+        git_ready.auto_commit("v1")
+        previous_stat = path.stat()
+
+        path.write_text("v2", encoding="utf-8")
+        os.utime(path, ns=(previous_stat.st_atime_ns, previous_stat.st_mtime_ns))
+
+        assert git_ready.auto_commit("v2") is not None
+        assert [commit.message for commit in git_ready.log()[:2]] == ["v2", "v1"]
+
     def test_does_not_create_empty_commits(self, git_ready):
         git_ready.auto_commit("nothing 1")
         git_ready.auto_commit("nothing 2")