fullClasspath in Runtime <<= (fullClasspath in Runtime, classDirectory in Compile) map { (cp, classes) => (cp.files map {
  f: File =>
    if (f.getName == classes.getName) {
      val result = new File(f.getParent + File.separator + "transformed-" + f.getName)
      if (result.exists) result else f
    } else f
}).classpath }

fullClasspath in Runtime := ...

fullClasspath in Runtime := (fullClasspath in Runtime).value.files.map {
  f: File =>
    if (f.getName == (classDirectory in Compile).value.getName) {
      val result = new File(f.getParent + File.separator + "transformed-" + f.getName)
      if (result.exists) result else f
    } else f
}.classpath

% sbt
> show runtime:fullClasspath
[info] List(Attributed(.../target/classes),
            Attributed(.../jars/scala-library-2.10.4.jar),
            Attributed(.../jars/asm-all-3.3.1.jar))
> set fullClasspath in Runtime := (fullClasspath in Runtime).value.files.filterNot(_.getName.containsSlice("asm")).classpath
> show runtime:fullClasspath
[info] List(Attributed(.../target/classes),
            Attributed(.../jars/scala-library-2.10.4.jar))

set fullClasspath in Runtime <<= (fullClasspath in Runtime) map
  {_.files.filterNot(_.getName.containsSlice("asm")).classpath}