This is due to https://bugs.eclipse.org/bugs/show_bug.cgi?id=520667[a limitation in Eclipse] that does not allow more than one module in one project.
It you want to do blackbox testing in Eclipse, you should move the integration tests to separate subprojects.

                        assert testProp == 'rootValue'
                    }
                }
            """.stripIndent()

            ['a', 'b', 'a:a1'].each {
                buildFile << """
                project(':${it}') {
                    task checkTestProp {
                        doLast {
                            assert testProp == '${expectedPropPerProject[it]}'
                        }
                    }

This is due to https://bugs.eclipse.org/bugs/show_bug.cgi?id=520667[a limitation in Eclipse] that does not allow more than one module in one project.
It you want to do blackbox testing in Eclipse, you should move the integration tests to separate subprojects.

        configurations.getByName(configurationName).incoming.resolutionResult.allComponents.asSequence()
            .projectDependenciesIdentifiers()
            .map { project(it.projectPath) }
            .withJavaBasePlugin()
            .allSourceSetsRoots()
            .map { it.relativeTo(rootDir).path }
            .toList()
    }

    private

    /**
     * Register a watchable hierarchy.
     *
     * Only locations within watchable hierarchies will be watched for changes.
     * This method is first called for the root directory of the root project.
     * It is also called for the root directories of included builds, and all other nested builds.
     */
    void registerWatchableHierarchy(File rootDirectoryForWatching);

    /**

     * consumer project.
     * <p>
     * Note: This property is about "build path", whatever it means in the scope of the consumer project. It is NOT
     * about Java classpath or anything alike. How artifact is being consumed depends heavily on the consumer project.
     * Resolver is and will remain agnostic of consumer project use cases.
     */

     * @throws org.gradle.api.InvalidUserDataException if type is null.
     */
    void setType(ResourceFilterType type);

    /**
     * Indicates whether this ResourceFilter applies recursively to all children of the project it is created on.  Default is true.
     */
    boolean isRecursive();

    /**
     * Sets whether this ResourceFilter applies recursively or not.
     */
    void setRecursive(boolean recursive);

    /**

        when:

        BuildEnvironment env
        GradleProject project
        withConnection {
            env = it.model(BuildEnvironment.class).setJavaHome(jdk.javaHome).get()
            project = it.model(GradleProject.class).setJavaHome(jdk.javaHome).get()
        }

        then:
        project.description.startsWith(env.java.javaHome.canonicalPath)
    }

     * consumer project.
     * <p>
     * Note: This property is about "build path", whatever it means in the scope of the consumer project. It is NOT
     * about Java classpath or anything alike. How artifact is being consumed depends heavily on the consumer project.
     * Resolver is and will remain agnostic of consumer project use cases.
     */

        when:
        BuildEnvironment env
        GradleProject project
        withConnection {
            env = it.model(BuildEnvironment.class).setJvmArguments('-Xmx200m', '-Xms100m').get()
            project = it.model(GradleProject.class).setJvmArguments('-Xmx200m', '-Xms100m').get()
        }

        then:
        def inputArgsInBuild = project.description.split('##') as List