Fixed a compilation problem with GCC4.7

GCC 4.7 appears to be very unforgiving when it comes to the scope of variables.
This change solves the bug, but should also be ported to the different patches.
Manual had been left behind!

Also, removed references to berlios.de
  adding missing figures
  the actual figures
README formatting improved
Merge pull request #2 from i-pi/docfix

Docfix
Merge pull request #3 from azag0/feat-readme

README formatting improved