Program: 180529
Project: 180529
Buggy source:
private void addGitLinks(URI location,JSONObject representation) throws URISyntaxException, JSONException, CoreException, IOException {
  JSONObject gitSection=new JSONObject();
  IPath targetPath=new Path(location.getPath());
  IPath path=new Path(GitServlet.GIT_URI + '/' + GitConstants.DIFF_RESOURCE+ '/'+ GitConstants.KEY_DIFF_DEFAULT).append(targetPath);
  URI link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_DIFF,link.toString());
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.STATUS_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_STATUS,link.toString());
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.INDEX_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_INDEX,link.toString());
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.COMMIT_RESOURCE).append(Constants.HEAD).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_COMMIT,link.toString());
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.REMOTE_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_REMOTE,link.toString());
  File gitDir=GitUtils.getGitDir(targetPath);
  Repository db=new FileRepository(gitDir);
  for (  Entry<String,Ref> refEntry : db.getRefDatabase().getRefs(Constants.R_REMOTES).entrySet()) {
    if (!refEntry.getValue().isSymbolic()) {
      Ref ref=refEntry.getValue();
      String shortName=Repository.shortenRefName(ref.getName());
      if (db.getBranch().equals(shortName.substring(Constants.DEFAULT_REMOTE_NAME.length() + 1))) {
        link=new URI(location.getScheme(),location.getAuthority(),GitRemoteHandlerV1.baseToRemoteLocation(link,2,shortName).getPath(),null,null);
        gitSection.put(GitConstants.KEY_DEFAULT_REMOTE_BRANCH,link);
        break;
      }
    }
  }
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.TAG_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_TAG,link.toString());
  representation.put(GitConstants.KEY_GIT,gitSection);
}

Fixed version (ground truth):
private void addGitLinks(URI location,JSONObject representation) throws URISyntaxException, JSONException, CoreException, IOException {
  JSONObject gitSection=new JSONObject();
  IPath targetPath=new Path(location.getPath());
  IPath path=new Path(GitServlet.GIT_URI + '/' + GitConstants.DIFF_RESOURCE+ '/'+ GitConstants.KEY_DIFF_DEFAULT).append(targetPath);
  URI link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_DIFF,link);
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.STATUS_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_STATUS,link);
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.INDEX_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_INDEX,link);
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.COMMIT_RESOURCE).append(Constants.HEAD).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_COMMIT,link);
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.REMOTE_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_REMOTE,link);
  File gitDir=GitUtils.getGitDir(targetPath);
  Repository db=new FileRepository(gitDir);
  for (  Entry<String,Ref> refEntry : db.getRefDatabase().getRefs(Constants.R_REMOTES).entrySet()) {
    if (!refEntry.getValue().isSymbolic()) {
      Ref ref=refEntry.getValue();
      String shortName=Repository.shortenRefName(ref.getName());
      if (db.getBranch().equals(shortName.substring(Constants.DEFAULT_REMOTE_NAME.length() + 1))) {
        link=new URI(location.getScheme(),location.getAuthority(),GitRemoteHandlerV1.baseToRemoteLocation(link,2,shortName).getPath(),null,null);
        gitSection.put(GitConstants.KEY_DEFAULT_REMOTE_BRANCH,link);
        break;
      }
    }
  }
  path=new Path(GitServlet.GIT_URI + '/' + GitConstants.TAG_RESOURCE).append(targetPath);
  link=new URI(location.getScheme(),location.getAuthority(),path.toString(),null,null);
  gitSection.put(GitConstants.KEY_TAG,link);
  representation.put(GitConstants.KEY_GIT,gitSection);
}