Make skill file writes atomic

[aydnOktay]

his PR hardens skill management operations by making all file writes atomic. The skill_manager_tool now uses a temporary file and os.replace() for writing SKILL.md and supporting files, preventing corruption if Hermes crashes or is interrupted mid-write. The change adds a _atomic_write_text() helper that handles temp file creation, content writing, and atomic replacement, and updates _create_skill, _edit_skill, _patch_skill, and _write_file to use it. Rollback operations during security scans are also atomic, ensuring skill files remain consistent even if errors occur

[teknium1]

Merged locally with contributor credit (739eb67). Clean, well-implemented atomic write pattern — thanks for the contribution! 🙏