SAMPLE = '''A great brown fox [13] jumped of a pile of lorem ipsum [4], [7]. He
met with a silver penguin, browsing the Linux Kernel Mailinglist [3]. They
debated other the question whether to start a C-program with "main (int argc,
char **argv)" or with "main (int argc, char *argv[])". Square brackets annoyed
them [9999]. Multiple references may exist to same targets [4].

@footnote:

[13] Al Fabetus: "On characters and animals", 1888, self published.
[4] Lorem Ipsum, <a href="http://en.wikipedia.org/wiki/Lorem_ipsum">Web Link</a>
[9999] Annoying Link.
[7] B. Fox: "More on Blind Text".
[3] Linux Kernel Maintainers: LKML
'''
import sys, re

def nodups(lst):
  new = []
  for x in lst:
    if x not in new:
      new.append(x)
  return new

def mkMap(lst):
  return dict([(ref, "[%d]" % (n+1)) for n, ref in enumerate(lst)])

def asNum(line):
  try:
    key, _ = line[1:].split(']', 1)
    key = int(key)
  except:
    key = line or None  # If line looks wrong, just return the raw line
  return key

def footnote(s, usebody=False):
  FOOTSPLIT = '\n@footnote:\n'
  body, foots = s.split(FOOTSPLIT)
  links = nodups(re.findall(r'\[\d+\]', body))
  targets = nodups(re.findall(r'\[\d+\]', foots))
  mapping = mkMap(links if usebody else targets) # Ref order of body xor foots
  # If Python < 2.5, could use:
  # mapping = mkMap((targets, links)[usebody])

  # Replace source->target footnote numbers
  def numsub(m):
    return mapping[m.group(1)]
  body = re.sub(r'(\[\d+\])', numsub , body)
  foots = re.sub(r'(\[\d+\])', numsub, foots)

  # May need to reorder target lines in foots
  if usebody:
    foots = '\n'.join(sorted(foots.splitlines(), key=asNum))

  return body + FOOTSPLIT + "\n" + foots.strip()

if __name__ == '__main__':
  if '--test' in sys.argv[1:]:
    print footnote(SAMPLE, usebody='-a' in sys.argv[1:])
  else:
    print footnote(sys.stdin.read(), usebody='-a' in sys.argv[1:])