fix(update): stop a timed-out git from leaving .git/index.lock behind

subprocess.run's timeout SIGKILLs only the direct git child, so the lock
is left behind and git's helpers are orphaned. On a slow SD card the same
pull then times out on every retry and recreates the lock, so removing it
by hand does not help.

- run_git starts git in its own session, stops the group with SIGTERM
  before SIGKILL, and clears the lock if nothing owns it. Update Code's
  pull, checkout, reset and stash go through it, with a 600s pull timeout.
- Read-only calls (describe --dirty, status, the update-check fetch) set
  GIT_OPTIONAL_LOCKS=0 so a timed-out poll cannot take the lock.
- A timed-out pull returns a clear error; a rebase left by an interrupted
  update is aborted before pulling.
- The manual-fix hint says to stop the services and kill running git.

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

test/test_update_prompts_restart.py

@@ -9,6 +9,7 @@ restart is owed, and the UI raises the existing restart-pending banner.
 import subprocess
 import sys
 from pathlib import Path
+import contextlib
 from unittest.mock import patch
 
 import pytest
@@ -20,6 +21,13 @@ from web_interface.blueprints import api_v3 as mod  # noqa: E402
 from web_interface.blueprints.api_v3 import api_v3  # noqa: E402
 
 
+@contextlib.contextmanager
+def _patched(fake):
+    """Fake git for both the plain subprocess calls and the timeout-safe runner."""
+    with patch.object(mod.subprocess, 'run', fake), patch.object(mod.git_index_lock, 'run_git', fake):
+        yield
+
+
 @pytest.fixture
 def client():
     app = Flask(__name__)
@@ -62,7 +70,7 @@ def _pull(client):
 
 class TestRestartIsRequestedWhenCodeChanged:
     def test_a_pull_that_moved_head_asks_for_a_restart(self, client):
-        with patch.object(mod.subprocess, 'run', _git(['aaa111', 'bbb222'])):
+        with _patched(_git(['aaa111', 'bbb222'])):
             data = _pull(client)
         assert data['status'] == 'success'
         assert data['restart_required'] is True, (
@@ -70,15 +78,14 @@ class TestRestartIsRequestedWhenCodeChanged:
             "nothing told the user to restart")
 
     def test_already_up_to_date_does_not(self, client):
-        with patch.object(mod.subprocess, 'run',
-                          _git(['aaa111', 'aaa111'], pull_out='Already up to date.\n')):
+        with _patched(_git(['aaa111', 'aaa111'], pull_out='Already up to date.\n')):
             data = _pull(client)
         assert data['status'] == 'success'
         assert data['restart_required'] is False, (
             "prompting after a no-op update trains users to ignore the prompt")
 
     def test_a_failed_pull_does_not(self, client):
-        with patch.object(mod.subprocess, 'run', _git(['aaa111'], pull_rc=1)):
+        with _patched(_git(['aaa111'], pull_rc=1)):
             data = _pull(client)
         assert data['status'] == 'error'
         assert data['restart_required'] is False
@@ -100,19 +107,18 @@ class TestUnitsAreRefreshedWithTheCode:
         return calls
 
     def test_an_update_that_moved_head_refreshes_the_units(self, client, refresh):
-        with patch.object(mod.subprocess, 'run', _git(['aaa111', 'bbb222'])):
+        with _patched(_git(['aaa111', 'bbb222'])):
             data = _pull(client)
         assert refresh == [True]
         assert data['unit_refresh']['status'] == 'refreshed'
         assert 'Service settings updated' in data['message']
 
     def test_nothing_new_touches_no_units(self, client, refresh):
-        with patch.object(mod.subprocess, 'run',
-                          _git(['aaa111', 'aaa111'], pull_out='Already up to date.\n')):
+        with _patched(_git(['aaa111', 'aaa111'], pull_out='Already up to date.\n')):
             data = _pull(client)
         assert refresh == [] and data['unit_refresh'] is None
 
     def test_a_failed_pull_touches_no_units(self, client, refresh):
-        with patch.object(mod.subprocess, 'run', _git(['aaa111'], pull_rc=1)):
+        with _patched(_git(['aaa111'], pull_rc=1)):
             data = _pull(client)
         assert refresh == [] and data['unit_refresh'] is None