fix: reduce file tool log noise

- treat git diff --cached --quiet rc=1 as an expected checkpoint state
  instead of logging it as an error
- downgrade expected write PermissionError/EROFS/EACCES failures out of
  error logging while keeping unexpected exceptions at error level
- add regression tests for both logging behaviors

tests/tools/test_checkpoint_manager.py

@@ -1,8 +1,10 @@
 """Tests for tools/checkpoint_manager.py — CheckpointManager."""
 
+import logging
 import os
 import json
 import shutil
+import subprocess
 import pytest
 from pathlib import Path
 from unittest.mock import patch
@@ -143,6 +145,12 @@ class TestTakeCheckpoint:
         result = mgr.ensure_checkpoint(str(work_dir), "initial")
         assert result is True
 
+    def test_successful_checkpoint_does_not_log_expected_diff_exit(self, mgr, work_dir, caplog):
+        with caplog.at_level(logging.ERROR, logger="tools.checkpoint_manager"):
+            result = mgr.ensure_checkpoint(str(work_dir), "initial")
+        assert result is True
+        assert not any("diff --cached --quiet" in r.getMessage() for r in caplog.records)
+
     def test_dedup_same_turn(self, mgr, work_dir):
         r1 = mgr.ensure_checkpoint(str(work_dir), "first")
         r2 = mgr.ensure_checkpoint(str(work_dir), "second")
@@ -375,6 +383,26 @@ class TestErrorResilience:
         result = mgr.ensure_checkpoint(str(work_dir), "test")
         assert result is False
 
+    def test_run_git_allows_expected_nonzero_without_error_log(self, tmp_path, caplog):
+        completed = subprocess.CompletedProcess(
+            args=["git", "diff", "--cached", "--quiet"],
+            returncode=1,
+            stdout="",
+            stderr="",
+        )
+        with patch("tools.checkpoint_manager.subprocess.run", return_value=completed):
+            with caplog.at_level(logging.ERROR, logger="tools.checkpoint_manager"):
+                ok, stdout, stderr = _run_git(
+                    ["diff", "--cached", "--quiet"],
+                    tmp_path / "shadow",
+                    str(tmp_path / "work"),
+                    allowed_returncodes={1},
+                )
+        assert ok is False
+        assert stdout == ""
+        assert stderr == ""
+        assert not caplog.records
+
     def test_checkpoint_failure_does_not_raise(self, mgr, work_dir, monkeypatch):
         """Checkpoint failures should never raise — they're silently logged."""
         def broken_run_git(*args, **kwargs):

tests/tools/test_file_tools.py

@@ -5,6 +5,7 @@ handling without requiring a running terminal environment.
 """
 
 import json
+import logging
 from unittest.mock import MagicMock, patch
 
 from tools.file_tools import (
@@ -87,13 +88,26 @@ class TestWriteFileHandler:
         mock_ops.write_file.assert_called_once_with("/tmp/out.txt", "hello world!\n")
 
     @patch("tools.file_tools._get_file_ops")
-    def test_exception_returns_error_json(self, mock_get):
+    def test_permission_error_returns_error_json_without_error_log(self, mock_get, caplog):
         mock_get.side_effect = PermissionError("read-only filesystem")
 
         from tools.file_tools import write_file_tool
-        result = json.loads(write_file_tool("/tmp/out.txt", "data"))
+        with caplog.at_level(logging.DEBUG, logger="tools.file_tools"):
+            result = json.loads(write_file_tool("/tmp/out.txt", "data"))
         assert "error" in result
         assert "read-only" in result["error"]
+        assert any("write_file expected denial" in r.getMessage() for r in caplog.records)
+        assert not any(r.levelno >= logging.ERROR for r in caplog.records)
+
+    @patch("tools.file_tools._get_file_ops")
+    def test_unexpected_exception_still_logs_error(self, mock_get, caplog):
+        mock_get.side_effect = RuntimeError("boom")
+
+        from tools.file_tools import write_file_tool
+        with caplog.at_level(logging.ERROR, logger="tools.file_tools"):
+            result = json.loads(write_file_tool("/tmp/out.txt", "data"))
+        assert result["error"] == "boom"
+        assert any("write_file error" in r.getMessage() for r in caplog.records)
 
 
 class TestPatchHandler: