Enhance lat_check MCP tool with optional scope parameter

Added

• Optional scope parameter (either md, code-refs, index or sections) for lat_check MCP tool. Allows for a more granular execution of the lat check command on the MCP server. Now the four sub-commands can be called individually.
  • lat check md
  • lat check code-refs
  • lat check index
  • lat check sections

Resolves https://github.com/1st1/lat.md/issues/42