Program: 161179
Project: 161179
Buggy source:
@Scheduled(fixedDelay=60 * 1000) public void incrementalUpdate(){
  logFileIndex.update(new IndexTemplate.WriteCallback(){
    @Override public void write(    final IndexWriter indexWriter,    final TaxonomyWriter taxonomyWriter) throws IOException {
      final Set<String> todaysIndexedFiles=Sets.newHashSet(Iterables.transform(logFileIndex.searchByDate(LocalDate.now()),new Function<LoggedUpdate,String>(){
        @Override public String apply(        final LoggedUpdate input){
          return input.getUpdateId();
        }
      }
));
      final String todaysFolder=LogFileIndex.DATE_FORMATTER.print(LocalDate.now());
      try {
        Files.walkFileTree(Paths.get(logDirectory),new SimpleFileVisitor<Path>(){
          @Override public FileVisitResult preVisitDirectory(          final Path dir,          final BasicFileAttributes attrs) throws IOException {
            if (dir.getFileName().toString().equals(todaysFolder)) {
              new DailyLogFolder(dir).processLoggedFiles(new LoggedUpdateProcessor<DailyLogEntry>(){
                @Override public boolean accept(                DailyLogEntry dailyLogEntry){
                  return INDEXED_LOG_ENTRIES.matcher(dailyLogEntry.getUpdateId()).matches() && !todaysIndexedFiles.contains(dailyLogEntry.getUpdateId());
                }
                @Override public void process(                DailyLogEntry dailyLogEntry,                String contents){
                  LogFileIndex.addToIndex(dailyLogEntry,contents,indexWriter);
                }
              }
);
              return FileVisitResult.SKIP_SUBTREE;
            }
            return FileVisitResult.CONTINUE;
          }
          @Override public FileVisitResult visitFileFailed(          Path file,          IOException e){
            LOGGER.info("String_Node_Str",file.toAbsolutePath(),e.getMessage());
            return FileVisitResult.CONTINUE;
          }
        }
);
      }
 catch (      IOException e) {
        LOGGER.error(e.getMessage(),e);
      }
    }
  }
);
}

Fixed version (ground truth):
@Scheduled(fixedDelay=60 * 1000) public void incrementalUpdate(){
  logFileIndex.update(new IndexTemplate.WriteCallback(){
    @Override public void write(    final IndexWriter indexWriter,    final TaxonomyWriter taxonomyWriter) throws IOException {
      final Set<String> todaysIndexedFiles=Sets.newHashSet(Iterables.transform(logFileIndex.searchByDate(LocalDate.now()),new Function<LoggedUpdate,String>(){
        @Override public String apply(        final LoggedUpdate input){
          return input.getUpdateId();
        }
      }
));
      final String todaysFolder=LogFileIndex.DATE_FORMATTER.print(LocalDate.now());
      try {
        Files.walkFileTree(Paths.get(logDirectory),new SimpleFileVisitor<Path>(){
          @Override public FileVisitResult preVisitDirectory(          final Path dir,          final BasicFileAttributes attrs) throws IOException {
            if (dir.getFileName().toString().equals(todaysFolder)) {
              new DailyLogFolder(dir).processLoggedFiles(new LoggedUpdateProcessor<DailyLogEntry>(){
                @Override public boolean accept(                DailyLogEntry dailyLogEntry){
                  return INDEXED_LOG_ENTRIES.matcher(dailyLogEntry.getUpdateId()).matches() && !todaysIndexedFiles.contains(dailyLogEntry.getUpdateId());
                }
                @Override public void process(                DailyLogEntry dailyLogEntry,                String contents){
                  LogFileIndex.addToIndex(dailyLogEntry,contents,indexWriter);
                }
              }
);
              return FileVisitResult.SKIP_SUBTREE;
            }
            return FileVisitResult.CONTINUE;
          }
          @Override public FileVisitResult visitFileFailed(          Path file,          IOException e){
            LOGGER.info("String_Node_Str",file.toAbsolutePath(),e.getMessage());
            return FileVisitResult.CONTINUE;
          }
        }
);
      }
 catch (      FileSystemException e) {
        if (!e.getReason().equals("String_Node_Str")) {
          LOGGER.error(e.getMessage(),e);
        }
      }
catch (      IOException e) {
        LOGGER.error(e.getMessage(),e);
      }
    }
  }
);
}