Program: 37394
Project: 37394
Buggy source:
/** 
 * Adds breakpoints to breakpoint manager. Deletes all breakpoints that are no longer listed. In the case of modified source, delete everything.
 * @param source source path of breakpoints
 * @param breakpoints full list of breakpoints that locates in this source file
 * @param sourceModified the source file are modified or not.
 * @return the full breakpoint list that locates in the source file
 */
public IBreakpoint[] setBreakpoints(String source,IBreakpoint[] breakpoints,boolean sourceModified){
  List<IBreakpoint> result=new ArrayList<>();
  HashMap<String,IBreakpoint> breakpointMap=this.sourceToBreakpoints.get(source);
  if (sourceModified && breakpointMap != null) {
    for (    IBreakpoint bp : breakpointMap.values()) {
      try {
        bp.close();
      }
 catch (      Exception e) {
        logger.severe(String.format("String_Node_Str",e));
      }
      this.breakpoints.remove(bp);
    }
    this.sourceToBreakpoints.put(source,null);
    breakpointMap=null;
  }
  if (breakpointMap == null) {
    breakpointMap=new HashMap<>();
    this.sourceToBreakpoints.put(source,breakpointMap);
  }
  List<IBreakpoint> toAdd=new ArrayList<>();
  List<Integer> visitedLineNumbers=new ArrayList<>();
  for (  IBreakpoint breakpoint : breakpoints) {
    IBreakpoint existed=breakpointMap.get(String.valueOf(breakpoint.lineNumber()));
    if (existed != null) {
      result.add(existed);
      visitedLineNumbers.add(existed.lineNumber());
      continue;
    }
 else {
      result.add(breakpoint);
    }
    toAdd.add(breakpoint);
  }
  List<IBreakpoint> toRemove=new ArrayList<>();
  for (  IBreakpoint breakpoint : breakpointMap.values()) {
    if (!visitedLineNumbers.contains(breakpoint.lineNumber())) {
      toRemove.add(breakpoint);
    }
  }
  removeBreakpointsInternally(source,toRemove.toArray(new IBreakpoint[0]));
  addBreakpointsInternally(source,toAdd.toArray(new IBreakpoint[0]));
  return result.toArray(new IBreakpoint[0]);
}

Fixed version (ground truth):
/** 
 * Adds breakpoints to breakpoint manager. Deletes all breakpoints that are no longer listed. In the case of modified source, delete everything.
 * @param source source path of breakpoints
 * @param breakpoints full list of breakpoints that locates in this source file
 * @param sourceModified the source file are modified or not.
 * @return the full breakpoint list that locates in the source file
 */
public IBreakpoint[] setBreakpoints(String source,IBreakpoint[] breakpoints,boolean sourceModified){
  List<IBreakpoint> result=new ArrayList<>();
  HashMap<String,IBreakpoint> breakpointMap=this.sourceToBreakpoints.get(source);
  if (sourceModified && breakpointMap != null) {
    for (    IBreakpoint bp : breakpointMap.values()) {
      try {
        bp.close();
      }
 catch (      Exception e) {
        logger.log(Level.SEVERE,String.format("String_Node_Str",e.toString()),e);
      }
      this.breakpoints.remove(bp);
    }
    this.sourceToBreakpoints.put(source,null);
    breakpointMap=null;
  }
  if (breakpointMap == null) {
    breakpointMap=new HashMap<>();
    this.sourceToBreakpoints.put(source,breakpointMap);
  }
  List<IBreakpoint> toAdd=new ArrayList<>();
  List<Integer> visitedLineNumbers=new ArrayList<>();
  for (  IBreakpoint breakpoint : breakpoints) {
    IBreakpoint existed=breakpointMap.get(String.valueOf(breakpoint.lineNumber()));
    if (existed != null) {
      result.add(existed);
      visitedLineNumbers.add(existed.lineNumber());
      continue;
    }
 else {
      result.add(breakpoint);
    }
    toAdd.add(breakpoint);
  }
  List<IBreakpoint> toRemove=new ArrayList<>();
  for (  IBreakpoint breakpoint : breakpointMap.values()) {
    if (!visitedLineNumbers.contains(breakpoint.lineNumber())) {
      toRemove.add(breakpoint);
    }
  }
  removeBreakpointsInternally(source,toRemove.toArray(new IBreakpoint[0]));
  addBreakpointsInternally(source,toAdd.toArray(new IBreakpoint[0]));
  return result.toArray(new IBreakpoint[0]);
}