You can also delete old (older than 90 days) undo files with the following in your .vimrc:

  let s:undos = split(globpath(&undodir, '*'), "\n")
  call filter(s:undos, 'getftime(v:val) < localtime() - (60 * 60 * 24 * 90)')
  call map(s:undos, 'delete(v:val)')