Program: 174717
Project: 174717
Buggy source:
public static void readSettings() throws IOException {
  if (!(new File("String_Node_Str").exists())) {
    return;
  }
  BufferedReader reader;
  try {
    reader=new BufferedReader(new FileReader("String_Node_Str"));
  }
 catch (  Exception ex) {
    FileUtils.log("String_Node_Str" + "String_Node_Str" + ex.getMessage());
    return;
  }
  if (reader == null) {
    return;
  }
  String line;
  String[] settingAndValue;
  List<String> enabledGlitches=new ArrayList<>();
  while ((line=reader.readLine()) != null) {
    if (line.startsWith("String_Node_Str")) {
      settingAndValue=line.replace("String_Node_Str","String_Node_Str").split("String_Node_Str");
      if ("String_Node_Str".equals(settingAndValue[1])) {
        Settings.getInitiallyAvailableItems().add(settingAndValue[0]);
      }
      if ("String_Node_Str".equals(settingAndValue[1])) {
        Settings.getNonRandomizedItems().add(settingAndValue[0]);
      }
    }
 else     if (line.startsWith("String_Node_Str")) {
      settingAndValue=line.replace("String_Node_Str","String_Node_Str").split("String_Node_Str");
      if (Boolean.valueOf(settingAndValue[1])) {
        enabledGlitches.add(settingAndValue[0]);
      }
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setShopRandomization(line.split("String_Node_Str")[1],false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setFullItemAccess(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setRequireSoftwareComboForKeyFairy(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setEnableDamageBoostRequirements(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setRandomizeForbiddenTreasure(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setLaMulanaBaseDir(line.substring(line.indexOf("String_Node_Str") + 1),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setBossDifficulty(line.split("String_Node_Str")[1],false);
    }
  }
  Settings.setEnabledGlitches(enabledGlitches,false);
}

Fixed version (ground truth):
public static void readSettings() throws IOException {
  if (!(new File("String_Node_Str").exists())) {
    return;
  }
  BufferedReader reader;
  try {
    reader=new BufferedReader(new FileReader("String_Node_Str"));
  }
 catch (  Exception ex) {
    FileUtils.log("String_Node_Str" + "String_Node_Str" + ex.getMessage());
    return;
  }
  if (reader == null) {
    return;
  }
  String line;
  String[] settingAndValue;
  List<String> enabledGlitches=new ArrayList<>();
  Set<String> initiallyAvailableItems=new HashSet<>();
  Set<String> nonRandomizedItems=new HashSet<>();
  while ((line=reader.readLine()) != null) {
    if (line.startsWith("String_Node_Str")) {
      settingAndValue=line.replace("String_Node_Str","String_Node_Str").split("String_Node_Str");
      if ("String_Node_Str".equals(settingAndValue[1])) {
        initiallyAvailableItems.add(settingAndValue[0]);
      }
      if ("String_Node_Str".equals(settingAndValue[1])) {
        nonRandomizedItems.add(settingAndValue[0]);
      }
    }
 else     if (line.startsWith("String_Node_Str")) {
      settingAndValue=line.replace("String_Node_Str","String_Node_Str").split("String_Node_Str");
      if (Boolean.valueOf(settingAndValue[1])) {
        enabledGlitches.add(settingAndValue[0]);
      }
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setShopRandomization(line.split("String_Node_Str")[1],false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setFullItemAccess(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setRequireSoftwareComboForKeyFairy(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setEnableDamageBoostRequirements(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setRandomizeForbiddenTreasure(Boolean.valueOf(line.split("String_Node_Str")[1]),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setLaMulanaBaseDir(line.substring(line.indexOf("String_Node_Str") + 1),false);
    }
 else     if (line.startsWith("String_Node_Str")) {
      Settings.setBossDifficulty(line.split("String_Node_Str")[1],false);
    }
  }
  Settings.setEnabledGlitches(enabledGlitches,false);
  Settings.setInitiallyAvailableItems(initiallyAvailableItems,false);
  Settings.setNonRandomizedItems(nonRandomizedItems,false);
}