Source generators trigger creation of incorrect source folders

Using either 1.6.0 or 1.7.0-SNAPSHOT, the presence of source generators causes extra sourceFolder entries to be added to the module. A simple example that demonstrates this issue:

import sbt._
import Keys._

object ApplicationBuild extends Build {
  val main = Project("foo", file(".")).settings(

    sourceGenerators in Compile += Def.task {
      val file1 = (sourceManaged in Compile).value / "one" / "Test.java"
      IO.write(file1, """
package one;
class Test {}
""")

      val file2 = (sourceManaged in Compile).value / "two" / "Test.java"
      IO.write(file2, """
package two;
class Test {}
""")

      Seq(file1, file2)
    }.taskValue
  )
}

This leads to a module file containing extra src_managed/main/one and src_managed/main/two source folders:

<sourceFolder url="file://$MODULE_DIR$/../target/scala-2.10/src_managed/main/one" isTestSource="false"/>
<sourceFolder url="file://$MODULE_DIR$/../target/scala-2.10/src_managed/main/two" isTestSource="false"/>
<sourceFolder url="file://$MODULE_DIR$/../target/scala-2.10/src_managed/main" isTestSource="false"/>

In the real world, this is causing problems with Play 2.3.1, leading to errors like this when compiling from IntelliJ:

Error:(7, 14) routes is already defined as object routes
public class routes {

mpeltonen / sbt-idea

Source generators trigger creation of incorrect source folders #310