Program: 52929
Project: 52929
Buggy source:
private Set<String> generateRoots(List<String> sourceFiles){
  final Set<String> roots=new HashSet<>();
  final RootsHelper helper=new RootsHelper();
  for (  String sourceFile : sourceFiles) {
    String path=dirname(sourceFile);
    if (!isNullOrEmpty(path)) {
      helper.addSourcePath(path);
    }
  }
  final List<String> paths=helper.getSortedSourcePaths();
  for (int index=0, size=paths.size(); index < size; ) {
    final String path=pathWithBuck(paths.get(index));
    if (path == null) {
      index+=1;
      continue;
    }
    int lowestCost=helper.excludesUnder(path);
    String bestRoot=path;
    String parent=dirname(path);
    while (!isNullOrEmpty(parent)) {
      int cost=helper.excludesUnder(parent);
      if (cost < lowestCost) {
        lowestCost=cost;
        bestRoot=parent;
      }
      parent=pathWithBuck(dirname(parent));
    }
    roots.add(bestRoot);
    index+=1;
    String prefix=guaranteeEndsWithFileSeparator(bestRoot);
    while (index < size && paths.get(index).startsWith(prefix)) {
      index+=1;
    }
  }
  return roots;
}

Fixed version (ground truth):
/** 
 * This is a complex routine that takes a list of source files and builds the best set of roots - symlinks to directories - that contains the source files. <p>Any folder with a   {@code BUCK} file could be a root: the best root is the one that requiresthe fewest  {@code excludedFolder} tags, but sometimes we need to pick a less-good root. If wehave  {@code foo/bar/baz/tom},   {@code foo/bar/baz/dick}, and   {@code foo/bar/harry}, the best root for   {@code foo/bar/baz/tom} and {@code foo/bar/baz/dick} may be {@code foo/bar/baz} whilethe best root for  {@code foo/bar/harry} may be {@code foo/bar} ... which would be the directorycontaining  {@code foo/bar/baz}, so we need to pick   {@code foo/bar} for {@code foo/bar/baz/tom}. <p>We do this in two passes. The first pass builds a set of candidates and a map from source directory index to candidate, where a candidate is the best root by   {@code excludedFolder}count. The second pass examines each candidate, and replaces it with the highest ancestor from the set of candidate values, if any.
 */
private Set<String> generateRoots(List<String> sourceFiles){
  final RootsHelper helper=new RootsHelper();
  for (  String sourceFile : sourceFiles) {
    String path=dirname(sourceFile);
    if (!isNullOrEmpty(path)) {
      helper.addSourcePath(path);
    }
  }
  final List<String> paths=helper.getSortedSourcePaths();
  final Set<String> candidates=new HashSet<>();
  final String[] candidateMap=new String[paths.size()];
  for (int index=0, size=paths.size(); index < size; ) {
    final String path=pathWithBuck(paths.get(index));
    if (path == null) {
      index+=1;
      continue;
    }
    int lowestCost=helper.excludesUnder(path);
    String bestRoot=path;
    String parent=dirname(bestRoot);
    while (!isNullOrEmpty(parent)) {
      int cost=helper.excludesUnder(parent);
      if (cost < lowestCost) {
        lowestCost=cost;
        bestRoot=parent;
      }
      parent=pathWithBuck(dirname(parent));
    }
    candidates.add(bestRoot);
    candidateMap[index]=bestRoot;
    index+=1;
    String prefix=guaranteeEndsWithFileSeparator(bestRoot);
    while (index < size && paths.get(index).startsWith(prefix)) {
      index+=1;
    }
  }
  final Set<String> roots=new HashSet<>();
  for (int index=0, size=paths.size(); index < size; ) {
    final String candidate=candidateMap[index];
    if (candidate == null) {
      index+=1;
      continue;
    }
    String bestRoot=candidate;
    String parent=dirname(bestRoot);
    while (!isNullOrEmpty(parent)) {
      if (candidates.contains(parent)) {
        bestRoot=parent;
      }
      parent=dirname(parent);
    }
    roots.add(bestRoot);
    index+=1;
    String prefix=guaranteeEndsWithFileSeparator(bestRoot);
    while (index < size && paths.get(index).startsWith(prefix)) {
      index+=1;
    }
  }
  return roots;
}