Buildship keeps overwriting .classpath

I'm using Gradle and Eclipse with the Buildship plugin.

Buildship creates the .classpath file for Eclipse to use. I need one classpath entry (com.gwtplugins.gwt.eclipse.core.GWT_CONTAINER) to appear after the org.eclipse.buildship.core.gradleclasspathcontainer entry, for class-loading reasons.

So the relevant part of my .classpath file should look like this (having the GWT_CONTAINER on the bottom).

<classpath>
 <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
 <classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer" />
 <classpathentry kind="con" path="com.gwtplugins.gwt.eclipse.core.GWT_CONTAINER"/>
</classpath>

Buildship always has the gradleclasspathcontainer on the last position. So I tried to change the sorting like this in my build.gradle (excerpt):

eclipse {
    classpath { 
        file {
            beforeMerged { classpath ->
                def gwtClasspath = classpath.entries.find { entry -> entry.path == 'com.gwtplugins.gwt.eclipse.core.GWT_CONTAINER' }
                classpath.entries.remove gwtClasspath
                classpath.entries << gwtClasspath
            }
        }
    }

When using ./gradlew eclipseClasspath, the .classpath file is created correctly. But as soon as Buildship runs, the file is again overwritten with the wrong ordering.

I also tried using whenMerged instead of beforeMerged, but that doesn't change anything.

Here's the output of Gradle when started by Buildship (e.g. by clicking on Gradle -> Refresh on the Eclipse project's properties):

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
See https://docs.gradle.org/4.5/userguide/command_line_interface.html#sec:command_line_warnings

CONFIGURE SUCCESSFUL in 0s
:cleanEclipseWtpComponent
:cleanEclipseWtpFacet
:cleanEclipseWtp
:eclipseWtpComponent
:eclipseWtpFacet
:eclipseWtp

Deprecated Gradle features were used in this build, making it incompatible with Gradle 5.0.
See https://docs.gradle.org/4.5/userguide/command_line_interface.html#sec:command_line_warnings

BUILD SUCCESSFUL in 0s
4 actionable tasks: 4 executed

It seems Buildship doesn't even execute the eclipseClasspath task, but does create the .classpath file by some other means.

How can I get Buildship to honor my wish to have the classpath sorted my way?

I found the solution on Gradle forums:

Buildship doesn't use the eclipseClasspath task, but reads the configuration and creates .classpath by its own means. The Gradle classpath is appended to the end of the classpath, if it's not yet defined. This happens after executing the whenMerged section. So the solution is to add the Gradle classpath manually:

eclipse {
   classpath {
        containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
   }
}