Program: 7739
Project: 7739
Buggy source:
private void fillTreeItemWithGitDirectory(RepositoryMapping m,TreeItem treeItem2,boolean isAlternative){
  if (m.getGitDir() == null)   treeItem2.setText(2,UIText.ExistingOrNewPage_SymbolicValueEmptyMapping);
 else {
    IPath container=m.getContainerPath();
    if (!container.isEmpty())     container=Path.fromOSString("String_Node_Str");
    IPath relativePath=container.append(m.getGitDir());
    if (isAlternative) {
      IPath withoutLastSegment=relativePath.removeLastSegments(1);
      IPath path;
      if (withoutLastSegment.isEmpty())       path=Path.fromPortableString("String_Node_Str");
 else       path=withoutLastSegment;
      treeItem2.setText(0,path.toString());
    }
    treeItem2.setText(2,relativePath.toString());
    try {
      IProject project=m.getContainer().getProject();
      FileRepository repo=new FileRepository(m.getGitDirAbsolutePath().toFile());
      File workTree=repo.getWorkTree();
      IPath workTreePath=Path.fromOSString(workTree.getAbsolutePath());
      if (workTreePath.isPrefixOf(project.getLocation())) {
        IPath makeRelativeTo=project.getLocation().makeRelativeTo(workTreePath);
        String repoRelativePath=makeRelativeTo.append("String_Node_Str").toPortableString();
        ObjectId headCommitId=repo.resolve(Constants.HEAD);
        if (headCommitId != null) {
          RevWalk revWalk=new RevWalk(repo);
          RevCommit headCommit=revWalk.parseCommit(headCommitId);
          RevTree headTree=headCommit.getTree();
          TreeWalk projectInRepo=TreeWalk.forPath(repo,repoRelativePath,headTree);
          if (projectInRepo != null) {
            treeItem2.setChecked(true);
          }
          revWalk.dispose();
        }
      }
      repo.close();
    }
 catch (    IOException e1) {
      Activator.logError("String_Node_Str",e1);
    }
  }
}

Fixed version (ground truth):
private void fillTreeItemWithGitDirectory(RepositoryMapping m,TreeItem treeItem,boolean isAlternative){
  if (m.getGitDir() == null)   treeItem.setText(2,UIText.ExistingOrNewPage_SymbolicValueEmptyMapping);
 else {
    IPath container=m.getContainerPath();
    if (!container.isEmpty())     container=Path.fromOSString("String_Node_Str");
    IPath relativePath=container.append(m.getGitDir());
    if (isAlternative) {
      IPath withoutLastSegment=relativePath.removeLastSegments(1);
      IPath path;
      if (withoutLastSegment.isEmpty())       path=Path.fromPortableString("String_Node_Str");
 else       path=withoutLastSegment;
      treeItem.setText(0,path.toString());
    }
    treeItem.setText(2,relativePath.toOSString());
    try {
      IProject project=m.getContainer().getProject();
      FileRepository repo=new FileRepository(m.getGitDirAbsolutePath().toFile());
      File workTree=repo.getWorkTree();
      IPath workTreePath=Path.fromOSString(workTree.getAbsolutePath());
      if (workTreePath.isPrefixOf(project.getLocation())) {
        IPath makeRelativeTo=project.getLocation().makeRelativeTo(workTreePath);
        String repoRelativePath=makeRelativeTo.append("String_Node_Str").toPortableString();
        ObjectId headCommitId=repo.resolve(Constants.HEAD);
        if (headCommitId != null) {
          RevWalk revWalk=new RevWalk(repo);
          RevCommit headCommit=revWalk.parseCommit(headCommitId);
          RevTree headTree=headCommit.getTree();
          TreeWalk projectInRepo=TreeWalk.forPath(repo,repoRelativePath,headTree);
          if (projectInRepo != null) {
            treeItem.setChecked(true);
          }
          revWalk.dispose();
        }
      }
      repo.close();
    }
 catch (    IOException e1) {
      Activator.logError("String_Node_Str",e1);
    }
  }
}