refactor: consolidate symlink-safe atomic replace into shared helper

Extract the islink/realpath guard from the 16743 fix into a single
atomic_replace() helper in utils.py, then migrate every os.replace()
call site in the codebase to use it.

The original PR #16777 correctly identified and fixed the bug, but
only patched 9 of ~24 call sites. The same bug class (managed
deployments that symlink state files silently losing the link on
every write) still existed at auth.json, sessions file, gateway
config, env_loader, webhook subscriptions, debug store, model
catalog, pairing, google OAuth, nous rate guard, and more.

Rather than add another 10+ copies of the same three-line guard,
consolidate into atomic_replace(tmp, target) which:
- resolves symlinks via os.path.realpath before os.replace
- returns the resolved real path so callers can re-apply permissions
- is a drop-in replacement for os.replace at the use sites

Changes:
- utils.py: new atomic_replace() helper + atomic_json_write /
  atomic_yaml_write now call it instead of inlining the guard
- 16 files: all os.replace() call sites migrated to atomic_replace()
  - agent/{google_oauth, nous_rate_guard, shell_hooks}.py
  - cron/jobs.py
  - gateway/{pairing, session, platforms/telegram}.py
  - hermes_cli/{auth, config, debug, env_loader, model_catalog, webhook}.py
  - tools/{memory_tool, skill_manager_tool, skills_sync}.py

Tests: tests/test_atomic_replace_symlinks.py pins the invariant for
atomic_replace + atomic_json_write + atomic_yaml_write, covers plain
files, first-time creates, broken symlinks, and permission preservation.

Refs #16743
Builds on #16777 by @vominh1919.

tools/memory_tool.py

@@ -33,6 +33,8 @@ from pathlib import Path
 from hermes_constants import get_hermes_home
 from typing import Dict, Any, List, Optional
 
+from utils import atomic_replace
+
 # fcntl is Unix-only; on Windows use msvcrt for file locking
 msvcrt = None
 try:
@@ -448,10 +450,7 @@ class MemoryStore:
                     f.write(content)
                     f.flush()
                     os.fsync(f.fileno())
-                # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
-                path_str = str(path)
-                real_path = os.path.realpath(path_str) if os.path.islink(path_str) else path_str
-                os.replace(tmp_path, real_path)
+                atomic_replace(tmp_path, path)
             except BaseException:
                 # Clean up temp file on any failure
                 try: