Manage Scopes Settings correctly

I tried adding an IntegrationTest configuration to my build by doing this in build.sbt:

lazy val IntegrationTest = config("it") extend(Test)

and then

EclipseKeys.configurations += IntegrationTest

The first line ensures that the integration tests can depend on code in the src/test/scala directory. In order for the scoped compiler to work correctly in these conditions, the src/it/scala folder needs to be compiled during the tests scope. This is set by adding the line

//src/it/scala=tests

to org.scala-ide.sdt.core.prefs. Unfortunately, whenever sbt eclipse is run, the org.scala-ide.sdt.core.prefs file gets overwritten, so even if I manually add this setting, it gets overwritten on a clean rebuild. It would be nice if this were inferred automatically, or at a minimum there were an additional configuration option to fix it.

Reproduce the setup in build.sbt and run sbt eclipse, then inspect how org.scala-ide.sdt.core.prefs is generated and overwritten. The work is done when the src/it/scala=tests setting is inferred or can be preserved through an explicit configuration option after a clean rebuild.