test: deflake CI and dev-machine flaky tests in bulk (11 tests, 10 files) (#61816)

* test: deflake CI and dev-machine flaky tests in bulk

Fixes ten distinct flake sources found by mining recent CI failures and
running the full suite on a dev machine with real user state:

CI-observed races:
- tests/conftest.py live-system guard: allow signal 0 (pure liveness
  probe) through _guarded_kill/_guarded_killpg. psutil.pid_exists()
  probes a just-killed grandchild reparented to init; the subtree check
  fails for it and the guard RuntimeError'd
  test_entire_tree_is_sigkilled_not_just_parent intermittently on
  unrelated PRs.

Hermeticity flakes (fail on dev machines with real state, pass on CI):
- agent/coding_context.py: _marker_root() now skips the shared temp
  root (tempfile.gettempdir()) like it skips $HOME — a stray
  /tmp/package.json flipped every tmp_path test into the coding
  posture (9 failures in test_coding_context.py).
- test_agent_guardrails.py: pin MAX_CONCURRENT_CHILDREN=3 via autouse
  monkeypatch instead of freezing the user's real config value at
  import time (import-time vs call-time config mismatch).
- test_web_tools_config.py: TestCheckWebApiKey now neutralizes the
  ddgs package probe and registry providers — the optional ddgs
  package in a dev venv lit up the fallback backend.
- test_credential_pool.py: block claude_code/hermes-oauth credential
  autodiscovery in the two pool-merge tests that assert exact id
  lists (a real ~/.claude/.credentials.json seeded an extra entry).
- test_modal_sandbox_fixes.py: clear _permanent_approved /
  _session_approved — the user's real command_allowlist silently
  approved the guard-escalation commands under test.
- test_setup_irc.py: stub prompt_checklist to select only the IRC row;
  the non-TTY cancel fallback re-ran the real configured platforms'
  interactive setup_fn, which hit input() under captured stdin.
- test_doctor.py: TestGitHubTokenCheck now patches the module-level
  HERMES_HOME constant (the file's established pattern) instead of
  only setenv — doctor was running PRAGMA integrity_check against the
  real multi-GB state.db and blowing the 300s per-file budget.

Latent atexit-duplication (same _enter_buffered_busy class as #34217):
- test_undo_command.py: drop importlib.reload(tui_gateway.server) in
  fixture teardown; reload re-registers the module's atexit hooks.
- test_session_platform_resolution.py: drop per-test reload of
  tui_gateway.server; every resolver reads env at call time.

* test: sentinel model value in ignore-user-config fallback assertion

With HERMES_IGNORE_USER_CONFIG=1, load_cli_config() falls back to the
repo-root cli-config.yaml (untracked, gitignored). On a dev machine that
file can legitimately set the same popular model the test hardcoded
(anthropic/claude-sonnet-4.6), flipping the != assertion locally while
CI (no cli-config.yaml) stayed green. Use an impossible sentinel model
name instead.

agent/coding_context.py

@@ -56,6 +56,7 @@ import logging
 import os
 import re
 import subprocess
+import tempfile
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Any, Optional
@@ -412,10 +413,18 @@ def _marker_root(cwd: Path) -> Optional[Path]:
     """
     current = cwd.resolve()
     home = _home()
+    # Shared world-writable temp roots are never project roots: a stray
+    # manifest in /tmp (left by any process) must not flip every session
+    # whose cwd lives under the temp dir into the coding posture. Same
+    # reasoning as the $HOME skip below.
+    try:
+        temp_root = Path(tempfile.gettempdir()).resolve()
+    except Exception:
+        temp_root = None
     for depth, parent in enumerate([current, *current.parents]):
         if depth > 6:
             break
-        if parent == home:
+        if parent == home or (temp_root is not None and parent == temp_root):
             continue
         for marker in _PROJECT_MARKERS:
             if (parent / marker).exists():