fix(core): font zip cache, monotonic timers, resolver back-off, and other core/common fixes (#654)

* fix(core): font zip cache, monotonic timers, resolver back-off, and other core/common fixes

- font_manager: a .zip font URL is served as its extracted font after a
  restart (the cached-file check returned the archive first); downloads
  use requests with a 30s timeout into a temp file + os.replace.
- api_helper / sync_manager: rate-limit and heartbeat/leader timeouts use
  time.monotonic(); last_request_time and the status file's ts stay
  wall-clock. set_on_new_cycle docstring no longer claims core uses it.
- logo_helper: the placeholder uses the same scaled box as a real logo.
- permission_utils: one _sudo_bash_candidates() helper (with the sudoers
  exact-argv rationale) shared by sudo_remove_directory, which now retries
  the next bash path on a sudo refusal, and install_requirements_file.
- dynamic_team_resolver: failed/empty fetch backs off 5 min; duplicate
  INFO log and contradictory docstring example fixed.
- element_style: scale default looked up through element aliases.
- background_data_service: cache-hit callback runs outside the lock.
- config_arrays: union-aware type check (["array","null"]); stale
  dotToNested() reference removed.
- auto_update_setup: non-dict auto_update reads as off; temp result file
  unlinked when the write fails.
- exceptions: constructors copy the caller's context dict.
- logging_config: StructuredFormatter json.dumps(default=str).
- error_aggregator: removed unused export_path/export_to_file/_auto_export.
- Docstrings: validate_file_upload max_size_mb, raise_on_errors.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix(sync): retry the status-file rename like the other atomic writers

On Windows os.replace can fail with "Access is denied" while a scanner
briefly holds the target open; config_manager_atomic._replace already
retries that (and re-raises at once on other platforms). The sync status
writer called os.replace directly, which made
test_concurrent_writers_each_use_their_own_temp_file flaky on Windows.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

test/test_api_helper.py

@@ -50,29 +50,51 @@ def helper(cache):
 class TestRateLimiting:
     def test_sleeps_for_remaining_interval(self, helper, monkeypatch):
         fake_time = MagicMock()
-        fake_time.time.side_effect = [102.0, 105.0]
+        fake_time.monotonic.side_effect = [102.0, 105.0]
+        fake_time.time.return_value = 5000.0
         monkeypatch.setattr(api_helper_module, 'time', fake_time)
 
         helper.set_rate_limit(5)
-        helper._last_request_time = 100.0
+        helper._last_request_monotonic = 100.0
         helper._enforce_rate_limit()
 
         # 2s elapsed of a 5s interval -> sleep the remaining 3s.
         fake_time.sleep.assert_called_once()
         assert fake_time.sleep.call_args[0][0] == pytest.approx(3.0)
-        assert helper._last_request_time == 105.0
+        assert helper._last_request_monotonic == 105.0
+        assert helper._last_request_time == 5000.0
 
     def test_no_sleep_when_interval_elapsed(self, helper, monkeypatch):
         fake_time = MagicMock()
-        fake_time.time.side_effect = [200.0, 201.0]
+        fake_time.monotonic.side_effect = [200.0, 201.0]
         monkeypatch.setattr(api_helper_module, 'time', fake_time)
 
         helper.set_rate_limit(5)
-        helper._last_request_time = 100.0
+        helper._last_request_monotonic = 100.0
         helper._enforce_rate_limit()
 
         fake_time.sleep.assert_not_called()
-        assert helper._last_request_time == 201.0
+        assert helper._last_request_monotonic == 201.0
+
+    def test_wall_clock_step_back_does_not_stall_requests(self, helper, monkeypatch):
+        # NTP stepping the wall clock back an hour between two requests must
+        # not turn into an hour-long "remaining interval" sleep.
+        wall = {"now": 10_000.0}
+        mono = {"now": 50.0}
+        sleeps = []
+        fake_time = MagicMock()
+        fake_time.time.side_effect = lambda: wall["now"]
+        fake_time.monotonic.side_effect = lambda: mono["now"]
+        fake_time.sleep.side_effect = sleeps.append
+        monkeypatch.setattr(api_helper_module, 'time', fake_time)
+
+        helper.set_rate_limit(5)
+        helper._enforce_rate_limit()
+        wall["now"] -= 3600
+        mono["now"] += 10
+        helper._enforce_rate_limit()
+
+        assert all(s <= 5 for s in sleeps)
 
 
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