Wrong defaults for CrossProject builds in EclipseKeys.eclipseOutput

There appears to be an issue with shared sources in ScalaJS crossProject builds with Eclipse.

Consider a standard setup of

lazy val test = crossProject.in(file(".")).
  settings(
    name := "Test",
    EclipseKeys.useProjectId := true
  ).
  jvmSettings(
    libraryDependencies += "org.scala-js" %% "scalajs-stubs" % scalaJSVersion % "provided"
  ).
  jsSettings(
    libraryDependencies += "org.scala-js" %%% "scalajs-dom" % "0.9.1"
  )

If I import into eclipse like this, Eclipse finds the shared folders, but it sets their output folders to the source folder. See (from .classpath in the JS project):

  <classpathentry kind="src" path="src/main/scala"/>
  <classpathentry kind="src" path="src/main/resources"/>
  <classpathentry kind="src" path="src/test/scala"/>
  <classpathentry kind="src" path="src/test/resources"/>
  <classpathentry output="-Users-lkroll-Documents-Programming-test-shared-src-main-scala" kind="src" path="-Users-lkroll-Documents-Programming-test-shared-src-main-scala"/>
  <classpathentry output="-Users-lkroll-Documents-Programming-test-shared-src-test-scala" kind="src" path="-Users-lkroll-Documents-Programming-test-shared-src-test-scala"/>

When I set eclipseOutput manually to some other folder, it generates the correct output, as seen below.

lazy val test = crossProject.in(file(".")).
  settings(
    name := "Test",
    EclipseKeys.useProjectId := true,
    EclipseKeys.eclipseOutput := Some("./etarget")
  ).
  jvmSettings(
    libraryDependencies += "org.scala-js" %% "scalajs-stubs" % scalaJSVersion % "provided"
  ).
  jsSettings(
    libraryDependencies += "org.scala-js" %%% "scalajs-dom" % "0.9.1"
  )

<classpathentry output="./etarget" kind="src" path="src/main/scala"/>
  <classpathentry output="./etarget" kind="src" path="src/main/resources"/>
  <classpathentry output="./etarget" kind="src" path="src/test/scala"/>
  <classpathentry output="./etarget" kind="src" path="src/test/resources"/>
  <classpathentry output="./etarget" kind="src" path="-Users-lkroll-Documents-Programming-test-shared-src-main-scala"/>
  <classpathentry output="./etarget" kind="src" path="-Users-lkroll-Documents-Programming-test-shared-src-test-scala"/>

I don't know how sbt-eclipse decides what output path to default to when eclipseOutput is None, but at least in this case it's not the right thing.
This might, of course, be an issue on the ScalaJS plugin side, I don't know.

Edit: Sorry forgot to write versions:

• sbt 0.13.12
• sbteclipse 5.1.0
• sbtscalajs 0.6.14

Reproduce the provided Scala.js crossProject setup with sbt 0.13.12, sbteclipse 5.1.0, and sbtscalajs 0.6.14. Inspect the generated .classpath entries when EclipseKeys.eclipseOutput is None and compare them with the manually configured output. Done means shared source entries no longer use their source folders as output paths.