Program: 86518
Project: 86518
Buggy source:
/** 
 * Apply the reporting and repository removal changes to the list of   {@link Project}'s given.
 */
@Override public Set<Project> applyChanges(final List<Project> projects,final ManipulationSession session) throws ManipulationException {
  final RepoReportingState state=session.getState(RepoReportingState.class);
  if (!session.isEnabled() || !state.isEnabled()) {
    logger.debug(getClass().getSimpleName() + "String_Node_Str");
    return Collections.emptySet();
  }
  final Set<Project> changed=new HashSet<>();
  Settings backupSettings=new Settings();
  Profile backupProfile=new Profile();
  backupProfile.setId("String_Node_Str");
  backupSettings.addActiveProfile("String_Node_Str");
  for (  final Project project : projects) {
    final String ga=ga(project);
    logger.info("String_Node_Str" + ga);
    final Model model=project.getModel();
    Iterator<Repository> it=model.getRepositories().iterator();
    while (it.hasNext()) {
      Repository repository=it.next();
      if (removeRepository(state,repository)) {
        backupProfile.addRepository(repository);
        it.remove();
        changed.add(project);
      }
    }
    it=model.getPluginRepositories().iterator();
    while (it.hasNext()) {
      Repository repository=it.next();
      if (removeRepository(state,repository)) {
        backupProfile.addPluginRepository(repository);
        it.remove();
        changed.add(project);
      }
    }
    if (model.getReporting() != null) {
      backupProfile.setReporting(model.getReporting());
      model.setReporting(null);
      changed.add(project);
    }
    final List<Profile> profiles=ProfileUtils.getProfiles(session,model);
    for (    final Profile profile : profiles) {
      Profile repoProfile=new Profile();
      repoProfile.setId(profile.getId());
      it=profile.getRepositories().iterator();
      while (it.hasNext()) {
        Repository repository=it.next();
        if (removeRepository(state,repository)) {
          repoProfile.addRepository(repository);
          it.remove();
          changed.add(project);
        }
      }
      it=profile.getPluginRepositories().iterator();
      while (it.hasNext()) {
        Repository repository=it.next();
        if (removeRepository(state,repository)) {
          repoProfile.addPluginRepository(repository);
          it.remove();
          changed.add(project);
        }
      }
      if (profile.getReporting() != null) {
        repoProfile.setReporting(profile.getReporting());
        profile.setReporting(null);
        changed.add(project);
      }
      if (!repoProfile.getRepositories().isEmpty() && !repoProfile.getPluginRepositories().isEmpty() && repoProfile.getReporting() != null) {
        backupSettings.addProfile(SettingsUtils.convertToSettingsProfile(repoProfile));
      }
    }
  }
  if (!backupProfile.getRepositories().isEmpty() && !backupProfile.getPluginRepositories().isEmpty() && backupProfile.getReporting() != null) {
    backupSettings.addProfile(SettingsUtils.convertToSettingsProfile(backupProfile));
  }
  File settingsFile=state.getRemovalBackupSettings();
  if (settingsFile == null) {
    String topDir=session.getTargetDir().getParentFile().getPath();
    settingsFile=new File(topDir,"String_Node_Str");
  }
  settingsWriter.update(backupSettings,settingsFile);
  return changed;
}

Fixed version (ground truth):
/** 
 * Apply the reporting and repository removal changes to the list of   {@link Project}'s given.
 */
@Override public Set<Project> applyChanges(final List<Project> projects,final ManipulationSession session) throws ManipulationException {
  final RepoReportingState state=session.getState(RepoReportingState.class);
  if (!session.isEnabled() || !state.isEnabled()) {
    logger.debug(getClass().getSimpleName() + "String_Node_Str");
    return Collections.emptySet();
  }
  final Set<Project> changed=new HashSet<>();
  Settings backupSettings=new Settings();
  Profile backupProfile=new Profile();
  backupProfile.setId("String_Node_Str");
  backupSettings.addActiveProfile("String_Node_Str");
  for (  final Project project : projects) {
    final String ga=ga(project);
    logger.info("String_Node_Str" + ga);
    final Model model=project.getModel();
    Iterator<Repository> it=model.getRepositories().iterator();
    while (it.hasNext()) {
      Repository repository=it.next();
      if (removeRepository(state,repository)) {
        backupProfile.addRepository(repository);
        it.remove();
        changed.add(project);
      }
    }
    it=model.getPluginRepositories().iterator();
    while (it.hasNext()) {
      Repository repository=it.next();
      if (removeRepository(state,repository)) {
        backupProfile.addPluginRepository(repository);
        it.remove();
        changed.add(project);
      }
    }
    if (model.getReporting() != null) {
      backupProfile.setReporting(model.getReporting());
      model.setReporting(null);
      changed.add(project);
    }
    final List<Profile> profiles=ProfileUtils.getProfiles(session,model);
    for (    final Profile profile : profiles) {
      Profile repoProfile=new Profile();
      repoProfile.setId(profile.getId());
      it=profile.getRepositories().iterator();
      while (it.hasNext()) {
        Repository repository=it.next();
        if (removeRepository(state,repository)) {
          repoProfile.addRepository(repository);
          it.remove();
          changed.add(project);
        }
      }
      it=profile.getPluginRepositories().iterator();
      while (it.hasNext()) {
        Repository repository=it.next();
        if (removeRepository(state,repository)) {
          repoProfile.addPluginRepository(repository);
          it.remove();
          changed.add(project);
        }
      }
      if (profile.getReporting() != null) {
        repoProfile.setReporting(profile.getReporting());
        profile.setReporting(null);
        changed.add(project);
      }
      if (!repoProfile.getRepositories().isEmpty() || !repoProfile.getPluginRepositories().isEmpty() || repoProfile.getReporting() != null) {
        backupSettings.addProfile(SettingsUtils.convertToSettingsProfile(repoProfile));
      }
    }
  }
  if (!backupProfile.getRepositories().isEmpty() || !backupProfile.getPluginRepositories().isEmpty() || backupProfile.getReporting() != null) {
    backupSettings.addProfile(SettingsUtils.convertToSettingsProfile(backupProfile));
    String settingsFilePath=state.getRemovalBackupSettings();
    if (!isEmpty(settingsFilePath)) {
      File settingsFile;
      if (settingsFilePath.equals("String_Node_Str")) {
        String topDir=session.getTargetDir().getParentFile().getPath();
        settingsFile=new File(topDir,settingsFilePath);
      }
 else {
        settingsFile=new File(settingsFilePath);
      }
      settingsWriter.update(backupSettings,settingsFile);
    }
  }
  return changed;
}