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

utils.py

@@ -99,8 +99,11 @@ def atomic_json_write(
             )
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, path)
-        _restore_file_mode(path, original_mode)
+        # Resolve symlinks so os.replace writes to the real file instead of
+        # replacing the symlink with a regular file (GitHub #16743).
+        real_path = os.path.realpath(path) if os.path.islink(path) else path
+        os.replace(tmp_path, real_path)
+        _restore_file_mode(real_path, original_mode)
     except BaseException:
         # Intentionally catch BaseException so temp-file cleanup still runs for
         # KeyboardInterrupt/SystemExit before re-raising the original signal.
@@ -150,8 +153,11 @@ def atomic_yaml_write(
                 f.write(extra_content)
             f.flush()
             os.fsync(f.fileno())
-        os.replace(tmp_path, path)
-        _restore_file_mode(path, original_mode)
+        # Resolve symlinks so os.replace writes to the real file instead of
+        # replacing the symlink with a regular file (GitHub #16743).
+        real_path = os.path.realpath(path) if os.path.islink(path) else path
+        os.replace(tmp_path, real_path)
+        _restore_file_mode(real_path, original_mode)
     except BaseException:
         # Match atomic_json_write: cleanup must also happen for process-level
         # interruptions before we re-raise them.