Alternate way of setting test classpath attributes. Replaces all changes in BuildPathManager.java, see https://git.eclipse.org/r/#/c/111091/

DefaultClasspathManagerDelegate.java

/*******************************************************************************
 * Copyright (c) 2008-2017 Sonatype, Inc.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 *      Sonatype, Inc. - initial API and implementation
 *******************************************************************************/

package org.eclipse.m2e.jdt.internal;

import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IPath;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.Path;

import org.apache.maven.artifact.Artifact;
import org.apache.maven.artifact.resolver.filter.ArtifactFilter;
import org.apache.maven.project.MavenProject;

import org.eclipse.m2e.core.MavenPlugin;
import org.eclipse.m2e.core.embedder.ArtifactKey;
import org.eclipse.m2e.core.project.IMavenProjectFacade;
import org.eclipse.m2e.core.project.IMavenProjectRegistry;
import org.eclipse.m2e.core.project.IProjectConfigurationManager;
import org.eclipse.m2e.core.project.configurator.AbstractProjectConfigurator;
import org.eclipse.m2e.core.project.configurator.ILifecycleMapping;
import org.eclipse.m2e.jdt.IClasspathDescriptor;
import org.eclipse.m2e.jdt.IClasspathEntryDescriptor;
import org.eclipse.m2e.jdt.IClasspathManager;
import org.eclipse.m2e.jdt.IClasspathManagerDelegate;
import org.eclipse.m2e.jdt.IJavaProjectConfigurator;


/**
 * DefaultClasspathManagerDelegate
 * 
 * @author igor
 */
public class DefaultClasspathManagerDelegate implements IClasspathManagerDelegate {
  private final IProjectConfigurationManager configurationManager;

  private final IMavenProjectRegistry projectManager;

  public DefaultClasspathManagerDelegate() {
    this.configurationManager = MavenPlugin.getProjectConfigurationManager();
    this.projectManager = MavenPlugin.getMavenProjectRegistry();
  }

  public void populateClasspath(final IClasspathDescriptor classpath, IMavenProjectFacade projectFacade, final int kind,
      final IProgressMonitor monitor) throws CoreException {

    addClasspathEntries(classpath, projectFacade, kind, monitor);

    for(IJavaProjectConfigurator configurator : getJavaProjectConfigurators(projectFacade, monitor)) {
      configurator.configureClasspath(projectFacade, classpath, monitor);
    }
  }

  private List<IJavaProjectConfigurator> getJavaProjectConfigurators(IMavenProjectFacade projectFacade,
      final IProgressMonitor monitor) throws CoreException {

    ArrayList<IJavaProjectConfigurator> configurators = new ArrayList<IJavaProjectConfigurator>();

    ILifecycleMapping lifecycleMapping = configurationManager.getLifecycleMapping(projectFacade);

    if(lifecycleMapping != null) {
      for(AbstractProjectConfigurator configurator : lifecycleMapping.getProjectConfigurators(projectFacade, monitor)) {
        if(configurator instanceof IJavaProjectConfigurator) {
          configurators.add((IJavaProjectConfigurator) configurator);
        }
      }
    }
    return configurators;
  }

  void addClasspathEntries(IClasspathDescriptor classpath, IMavenProjectFacade facade, int kind,
      IProgressMonitor monitor) throws CoreException {
    ArtifactFilter scopeFilter;

    if(BuildPathManager.CLASSPATH_RUNTIME == kind) {
      // ECLIPSE-33: runtime+provided scope
      // ECLIPSE-85: adding system scope
      scopeFilter = new ArtifactFilter() {
        public boolean include(Artifact artifact) {
          return BuildPathManager.SCOPE_FILTER_RUNTIME.include(artifact)
              || Artifact.SCOPE_PROVIDED.equals(artifact.getScope())
              || Artifact.SCOPE_SYSTEM.equals(artifact.getScope());
        }
      };
    } else {
      // ECLIPSE-33: test scope (already includes provided)
      scopeFilter = BuildPathManager.SCOPE_FILTER_TEST;
    }

    MavenProject mavenProject = facade.getMavenProject(monitor);
    Set<Artifact> artifacts = mavenProject.getArtifacts();

    Map<IPath, ProjectTestAttributes> projectTestAttributes = new HashMap<>(artifacts.size());

    for(Artifact a : artifacts) {
      if(!scopeFilter.include(a) || !a.getArtifactHandler().isAddedToClasspath()) {
        continue;
      }

      // project
      IMavenProjectFacade dependency = projectManager.getMavenProject(a.getGroupId(), a.getArtifactId(),
          a.getBaseVersion());
      if(dependency != null && dependency.getProject().equals(facade.getProject())) {
        continue;
      }

      IClasspathEntryDescriptor entry = null;

      if(dependency != null && dependency.getFullPath(a.getFile()) != null) {
        IPath projectPath = dependency.getFullPath();
        entry = classpath.addProjectEntry(projectPath);
        ProjectTestAttributes testAttributes = projectTestAttributes.get(projectPath);
        if(testAttributes == null) {
          testAttributes = new ProjectTestAttributes(isTestScope(a), !isTestArtifact(a));
          projectTestAttributes.put(projectPath, testAttributes);
        } else {
          testAttributes.isTest &= isTestScope(a);
          testAttributes.excludeTestSources &= !isTestArtifact(a);
        }

      } else {
        File artifactFile = a.getFile();
        if(artifactFile != null /*&& artifactFile.canRead()*/) {
          entry = classpath.addLibraryEntry(Path.fromOSString(artifactFile.getAbsolutePath()));
          entry.setClasspathAttribute(IClasspathManager.TEST_ATTRIBUTE, isTestScope(a) ? "true" : null);
        }
      }

      if(entry != null) {
        entry.setArtifactKey(new ArtifactKey(a.getGroupId(), a.getArtifactId(), a.getBaseVersion(), a.getClassifier()));
        entry.setScope(a.getScope());
        entry.setOptionalDependency(a.isOptional());
      }
    }

    //2nd pass to set project test related attributes
    projectTestAttributes.forEach((entryPath, testAttributes) -> {
      //the classpath definitely has an entry matching the path
      IClasspathEntryDescriptor descriptor = findClasspathDescriptor(classpath, entryPath);
      descriptor.setClasspathAttribute(IClasspathManager.TEST_ATTRIBUTE, (testAttributes.isTest) ? "true" : null);
      descriptor.setClasspathAttribute(IClasspathManager.WITHOUT_TEST_CODE,
          (testAttributes.excludeTestSources) ? "true" : null);
    });
  }

  private boolean isTestScope(Artifact a) {
    return Artifact.SCOPE_TEST.equals(a.getScope());
  }

  private boolean isTestArtifact(Artifact a) {
    return BuildPathManager.CLASSIFIER_TESTS.equals(a.getClassifier()) || "test-jar".equals(a.getType());
  }

  private IClasspathEntryDescriptor findClasspathDescriptor(IClasspathDescriptor classpath, IPath p) {
    return classpath.getEntryDescriptors().stream().filter(e -> p.equals(e.getPath())).findFirst().orElse(null);
  }

  static class ProjectTestAttributes {
    ProjectTestAttributes(boolean isTest, boolean excludeTestSources) {
      this.isTest = isTest;
      this.excludeTestSources = excludeTestSources;
    }

    boolean isTest;

    boolean excludeTestSources;
  }

}

I think it works, and it avoid the extra conversion to a IClasspathEntryDescriptor and back, but it is essential that uniquePaths is true for the ClasspathDescriptor that is used when this is called (which it is, but it doesn't feel good to have this hidden requirement)
And unfortunately, I think making the entries unique in ClasspathDescriptor is a broken approach (because as I wrote somewhere, you'll get an classpath entry at the position of the first entry for the project, but with the attributes of the second entry)

I've tried it with a larger workspace and it didn't work correctly (I got some compilation errors).
From a quick look: Is there a negation messing here (there is one in the constructor call):
testAttributes.excludeTestSources &= isTestArtifact(a);