To prevent Front Matter CMS from including specific files and folders, you can provide the paths to be excluded in excludePaths under frontMatter.content.pageFolders:

{
  "frontMatter.content.pageFolders": [
    {
      "title": "Posts",
      "path": "[[workspace]]/content/posts",
      "previewPath": "posts",
      "contentTypes": ["Post (default)"],
      "excludePaths": [
        "_*.*" // Exclude all files starting with an underscore
      ]
    }
  ]
}

I use this to exclude _index.md files from Front Matter.