fix: preserve symlinks during atomic file writes (#16743)

os.replace(tmp, path) replaces the symlink itself with a regular file,
breaking users who symlink config.yaml, SOUL.md, or .env from ~/.hermes/
to a dotfiles repo or managed profile package.

Fix: resolve symlinks via os.path.realpath() before os.replace(), so the
real file is overwritten in-place while the symlink survives.

Fixed in 7 files covering all os.replace call sites:
- utils.py (atomic_json_write, atomic_yaml_write — fixes save_config)
- hermes_cli/config.py (env sanitizer, save_env_value, remove_env_value)
- tools/skill_manager_tool.py (_atomic_write_text — SOUL.md writes)
- tools/memory_tool.py (memory file writes)
- tools/skills_sync.py (manifest writes)
- cron/jobs.py (job state + output file writes)
- agent/shell_hooks.py (hook file writes)

Fixes NousResearch/hermes-agent#16743

cron/jobs.py

@@ -367,7 +367,9 @@ def save_jobs(jobs: List[Dict[str, Any]]):
             json.dump({"jobs": jobs, "updated_at": _hermes_now().isoformat()}, f, indent=2)
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, JOBS_FILE)
+        # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
+        real_path = os.path.realpath(JOBS_FILE) if os.path.islink(JOBS_FILE) else JOBS_FILE
+        os.replace(tmp_path, real_path)
         _secure_file(JOBS_FILE)
     except BaseException:
         try:
@@ -863,7 +865,9 @@ def save_job_output(job_id: str, output: str):
             f.write(output)
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, output_file)
+        # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
+        real_path = os.path.realpath(output_file) if os.path.islink(output_file) else output_file
+        os.replace(tmp_path, real_path)
         _secure_file(output_file)
     except BaseException:
         try: