include() BEFORE layouts()

build.js

const Metalsmith = require('metalsmith');
const layouts     = require( 'metalsmith-layouts' )
const markdown = require('metalsmith-markdown')
const include = require('metalsmith-include')

const config = {
  source: 'src',
  buildPath: 'public'
}

Metalsmith(__dirname)
  .source( config.source )
  .destination( config.buildPath )
  .clean(true)
  .use(markdown({
    html: true,
    xhtmlOut: true,
    typographer: true,
    linkify: true
  }))
  .use(include({
    deletePartials: true
  }))
  .use(layouts({
    engine: 'pug',
    pretty: true,
    directory: 'templates'
  }))
  .build(function(err, files){
    if (err) {
      console.log('ERROR:',err)
      return
    }
     
    console.log( 'Build Completed' )
    console.log( 'Files:', Object.keys( files ) )
  })

/**
 * Resulting content of public/home.html
<!-- Begin: home.pug-->
<div class="main"><h3 id="welcome-to-my-website-">Welcome to my website!</h3>
<h4 id="thanks-for-visiting-">Thanks for visiting!</h4>

</div>
<!-- End: home.pug-->
*/