// Perform apply of configuration changes.  This rewrites out the current known list of
  // configurations
  // with any changes currently that have been made to them.  If a configuration has been renamed,
  // but this
  // has not yet been confirmed by the end-user, then only the changes to the configuration are
  // made.  The
  // name currently remains the same in the output file.
  public synchronized void applyConfigs(String projectName, ICConfigurationDescription[] cfgds) {
    try {
      IWorkspaceRoot root = ResourcesPlugin.getWorkspace().getRoot();
      IResource res = root.findMember(projectName, false);
      if (res == null || res.getType() != IResource.PROJECT) {
        AutotoolsPlugin.logErrorMessage(
            ConfigureMessages.getFormattedString(CFG_CANT_SAVE, new String[] {projectName}));
        return;
      }
      IProject project = (IProject) res;
      IPath output = project.getLocation().append(CFG_FILE_NAME);
      File f = output.toFile();
      if (!f.exists()) f.createNewFile();
      if (f.exists()) {
        try (PrintWriter p = new PrintWriter(new BufferedWriter(new FileWriter(f)))) {
          Map<String, IAConfiguration> cfgs = getSavedConfigs(project);
          if (cfgs == null) return;
          p.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); // $NON-NLS-1$
          p.println("<configurations>"); // $NON-NLS-1$
          Option[] optionList = AutotoolsConfiguration.getOptionList();
          HashSet<String> savedIds = new HashSet<>();
          setSyncing(true);
          for (int x = 0; x < cfgds.length; ++x) {
            ICConfigurationDescription cfgd = cfgds[x];
            @SuppressWarnings("unused")
            CConfigurationData data = cfgd.getConfigurationData();
            String id = cfgd.getId();
            savedIds.add(id);
            IAConfiguration cfg = getTmpConfiguration(project, cfgd);
            cfgs.put(
                id,
                cfg); // add to list in case we have a new configuration not yet added to Project
                      // Description
            p.println("<configuration id=\"" + id + "\">"); // $NON-NLS-1$ //$NON-NLS-2$
            for (int j = 0; j < optionList.length; ++j) {
              Option option = optionList[j];
              IConfigureOption opt = cfg.getOption(option.getName());
              if (!opt.isCategory())
                p.println(
                    "<option id=\""
                        + option.getName()
                        + "\" value=\""
                        + opt.getValue()
                        + "\"/>"); //$NON-NLS-1$ //$NON-NLS-2$ // $NON-NLS-3$
            }
            p.println("</configuration>"); // $NON-NLS-1$
            syncNameField(cfgd);
          }
          setSyncing(false);

          // Put all the remaining configurations already saved back into the file.
          // These represent deleted configurations, but confirmation has not occurred.
          for (Entry<String, IAConfiguration> i : cfgs.entrySet()) {
            String id = i.getKey();
            // A remaining id won't appear in our savedIds list.
            if (!savedIds.contains(id)) {
              IAConfiguration cfg = i.getValue();
              p.println("<configuration id=\"" + id + "\">"); // $NON-NLS-1$ //$NON-NLS-2$
              for (int j = 0; j < optionList.length; ++j) {
                Option option = optionList[j];
                IConfigureOption opt = cfg.getOption(option.getName());
                if (!opt.isCategory())
                  p.println(
                      "<option id=\""
                          + option.getName()
                          + "\" value=\""
                          + opt.getValue()
                          + "\"/>"); //$NON-NLS-1$ //$NON-NLS-2$ // $NON-NLS-3$
              }
              p.println("</configuration>"); // $NON-NLS-1$
            }
          }
          p.println("</configurations>");
        }
      }
    } catch (IOException e) {
      AutotoolsPlugin.log(e);
    }
  }