{
  resolve: `gatsby-source-filesystem`,
  options: {
    name: `pages`,
    path: `${__dirname}/src/pages/`,
  },
},
{
  resolve: `gatsby-source-filesystem`,
  options: {
    name: `posts`,
    path: `${__dirname}/src/posts/`,
  },
},

Here, the name will not be used; instead, the parent folder will be used.

query MyQuery {
  allMarkdownRemark(filter: {fileAbsolutePath: {regex: "/(posts)/"  }}) {
    nodes {
      id
    }
  }
}