fix: add cwd to MCP config, fix skills path, handle JSONC configs

- Add cwd field to MCP server entry so clients can find graph.db
  (closes #325)
- Write skills to .claude/skills/<name>/skill.md subdirectory format
  matching Claude Code's expected layout (closes #360)
- Handle JSONC (comments, trailing commas) in editor config files like
  Zed's settings.json — skip instead of overwriting (closes #344)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>