Scala.js compilation destination

You can configure the Scala.js SBT plugin to output the JavaScript file in folder of your choosing. For example like this:

// configure a specific directory for scalajs output
val scalajsOutputDir = Def.settingKey[File]("directory for javascript files output by scalajs")

// make all JS builds use the output dir defined later
lazy val js2jvmSettings = Seq(fastOptJS, fullOptJS, packageJSDependencies) map { packageJSKey =>
  crossTarget in(js, Compile, packageJSKey) := scalajsOutputDir.value
}
// instantiate the JVM project for SBT with some additional settings
lazy val jvm: Project = sharedProject.jvm.settings(js2jvmSettings: _*).settings(
  // scala.js output is directed under "web/js" dir in the jvm project
  scalajsOutputDir := (classDirectory in Compile).value / "web" / "js",

This will also store -jsdeps.js and .js.map files in the same folder, in case you want to use those in your web app.

For a more complete example, check out this tutorial which addresses many other issues of creating a more complex Scala.js application.

You can simply set the artifactPath of the fastOptJS task (or the fullOptJS task) to the (managed) resources directory of your JVM project:

// In the JS project's settings
artifactPath in fastOptJS in Compile :=
  (resourceManaged in jvm in Compile).value /
    ((moduleName in fastOptJS).value + "-fastopt.js"))

This will put it in the directory, if the you run the fastOptJS task. However, it will not be included in sbt's resources task and it will not automatically be triggered, if you launch your server. Therefore:

// In the JVM project's settings
resources in Compile += (fastOptJS in js).value.data

A couple of notes:

• The first step is only necessary, if your web-server does only serve specific directories. Otherwise the second one is enough, as this adds the file to the resources already; where it lies is secondary.
• Setting the crossTarget, as in @ochrons' answer will also output all the .class and .sjsir files in the resource directory.
• Have a look at Vincent Munier's sbt-play-scalajs for out-of-the-box sbt-web / Scala.js integration (it follows a slightly different approach: It copies the file from the js project, rather than directly placing it in the JVM project. Useful if you have multiple JVM projects).