Honestly the index seems as much a liability as a boon. Keeping the context clean and focused is one of the most important things for getting the best out of lmms. For now I prefer just adding my md files to the context whenever I deem them relevant.

Skills are much simpler than mcps, which are hopelessly overengineered, but even skills seem unnecessarily overengineered. You could fix the skill index taking up place in the context, by just making it a tool available to the agent (but not an mcp!).