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

hermes_cli/config.py

@@ -3666,7 +3666,9 @@ def sanitize_env_file() -> int:
             f.writelines(sanitized)
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, env_path)
+        # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
+        real_path = os.path.realpath(env_path) if os.path.islink(env_path) else env_path
+        os.replace(tmp_path, real_path)
     except BaseException:
         try:
             os.unlink(tmp_path)
@@ -3769,7 +3771,9 @@ def save_env_value(key: str, value: str):
             f.writelines(lines)
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, env_path)
+        # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
+        real_path = os.path.realpath(env_path) if os.path.islink(env_path) else env_path
+        os.replace(tmp_path, real_path)
         # Restore original permissions before _secure_file may tighten them.
         if original_mode is not None:
             try:
@@ -3825,7 +3829,9 @@ def remove_env_value(key: str) -> bool:
                 f.writelines(new_lines)
                 f.flush()
                 os.fsync(f.fileno())
-            os.replace(tmp_path, env_path)
+            # Resolve symlinks so os.replace writes to the real file (GitHub #16743).
+            real_path = os.path.realpath(env_path) if os.path.islink(env_path) else env_path
+            os.replace(tmp_path, real_path)
             if original_mode is not None:
                 try:
                     os.chmod(env_path, original_mode)