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

tools/memory_tool.py

@@ -448,7 +448,10 @@ class MemoryStore:
                     f.write(content)
                     f.flush()
                     os.fsync(f.fileno())
-                os.replace(tmp_path, str(path))  # Atomic on same filesystem
+                # 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)
             except BaseException:
                 # Clean up temp file on any failure
                 try: