When I started with Elm and Phoenix I put Elm code into web directory and now when moving towards Phoenix 1.3 I kept this structure. So now Elm code is in lib/my_app/web/elm
brunch-config.js and package.json are in assets directory.
Elm part in brunch-config.js looks like this:

elmBrunch: {
      elmFolder: "../lib/my_app/web/elm",
      mainModules: ["Main.elm"],
      outputFolder: "../../../../assets/js"
    }

I have also added Elm path to (still brunch-config.js):

watched: [ "static", "css", "js", "vendor", "../lib/my_app/web/elm"],

I have modified package.json according to Phoenix upgrade instruction but I had to update devDependencies.
For this I created new Phoenix application using mix phx.new and I copied this part of a package.json
Now it looks like this:

{
  "repository": {},
  "license": "MIT",
  "scripts": {
    "deploy": "brunch build --production",
    "watch": "brunch watch --stdin"
  },
  "dependencies": {
    "phoenix": "file:../deps/phoenix",
    "phoenix_html": "file:../deps/phoenix_html"
  },
  "devDependencies": {
    "babel-brunch": "6.0.6",
    "brunch": "2.10.7",
    "clean-css-brunch": "2.10.0",
    "css-brunch": "2.10.0",
    "elm-brunch": "^0.8.0",
    "uglify-js-brunch": "2.1.1"
  }
}

Last thing I did was to update assets/js/app.js I had to add import Elm from "./main.js

import Elm from "./main.js"
const elmDiv = document.getElementById('elm-main')
   , elmApp = Elm.Main.embed(elmDiv)

Before it worked for me even without this import line, maybe it should work without anyhow, I’ll try.

Please let me know if you need more information.

I am using 1.3-rc.0. I have this directory structure:

assets/
    elm-package.json
    package.json
    brunch-config.js
    js/
    css/
    elm/
        Main.elm

I have elm, elm-css, elm-brunch, and elm-css-brunch installed:

npm install elm elm-css elm-brunch elm-css-brunch --save-dev

Here’s my brunch config (note I am also using elm-css):

I have my elm folder in the directory my_app/lib/my_app/web/elm.

I’m not using elmCss. The only 2 parts of my brunch config I changed that were relevant to elm are:

paths: {
    watched: ["static", "css", "js", "vendor", "../lib/my_app/web/elm"],
    ...

and

plugins: {
    babel: {
      ...
    },
    elmBrunch: {
      elmFolder: "../lib/my_app/web/elm",
      mainModules: ["Main.elm"],
      outputFolder: "../../../../assets/js",
      outputFile: 'elm.js',
      makeParameters: ["--warn"]
    }

I should probably move my elm folder to my_app/assets/elm like @dustinfarris though .

And at the top of my_app/assets/js/app.js I have import Elm from './elm.js';